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staden-lg/src/bap/dbsysnew.f

5041 lines
158 KiB
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C 26-1-93 added new consensus routine
C added file busy check
C 9-7-92 Changed remove contig line to remove all readings as well
C 4-6-92 Added pad shifting routine
C 6-4-92 fixed a bug in autocn revealed by new update method:
C for some cases where more than 2 overlaps were being found
C i was moving the wrong arrays around!
C 2-4-92 added new dbauto with new update consensus method
C and new consensus calculation
C 2-4-92 brought uptodate with dap
C 29.05.91 IMPLEMENTED REMOVE GEL READING
C 21-8-91 Added routines to find internal overlaps
C 2-9-91 Fixed bug in copytg
C 8-11-91 fixed bugs in "find internal joins"
C 23-Jun-92 COPYTAG - params to READCC and WRITCC in wrong order
C
SUBROUTINE NEWCON(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
+NGELS,NCONTS,MAXGEL,LLINO,LINCON,KOPT,
+TEMP3,SEQ1,MAXSEQ,SEQ2,SEQ3,
+MAXGLM,MAXGL2,CHRSIZ,ECHRSZ,
+ILADD,IRADD,MAXCON,
+KBIN,KBOUT,IDEV1,IDEV2,IDEV3,IDEV,
+IHELPS,IHELPE,HELPF,IDEVH,NAMARC,NAMPRO,FILE,
+PERCD,IDM,IDEVC,IDEVT)
INTEGER CHRSIZ,ECHRSZ,RREG
INTEGER RELPG(MAXDB)
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
INTEGER TEMP3(ECHRSZ,MAXGL2),ANS
INTEGER ILADD(MAXCON),IRADD(MAXCON)
CHARACTER SEQ3(MAXGLM)
CHARACTER SEQ1(MAXSEQ),SEQ2(MAXGLM)
CHARACTER NAMARC*(*),NAMPRO*(*),FILE*(*),HELPF*(*)
PARAMETER (MAXPRM = 6)
CHARACTER PROMPT(2)*(MAXPRM)
IF(NGELS.LT.1) RETURN
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ TEMP3,IERR,KBOUT)
IF(IERR.GT.1) RETURN
PROMPT(1) = 'Staden'
PROMPT(2) = 'FASTA'
C
C idim is current consensus length
C
IDIM = 0
ANS = 0
IWING = 0
FILE = ' '
CALL OPENF1(IDEV,FILE,1,IOK,KBIN,KBOUT,
+'Name for consensus file',
+IHELPS,IHELPE,FILEH,IDEVH)
IF(IOK.NE.0)RETURN
IF (KOPT.EQ.1) THEN
CALL YESNO(I,'Use clipped data',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(I.LT.0) GO TO 400
IF(I.EQ.0) THEN
MN = 1
MX = MAXGEL
IWING = 100
CALL GETINT(MN,MX,IWING,
+ 'Window size for good data scan',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) GO TO 400
IWING = IVAL
MN = 1
MX = MIN(100,IWING)
NBAD = MIN(IWING,5)
CALL GETINT(MN,MX,NBAD,
+ 'Maximum number of dashes in scan window',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) GO TO 400
NBAD = IVAL
END IF
END IF
CALL YESNO(ANS,'Make consensus for whole database',
+IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(ANS.LT.0) GO TO 400
IF(ANS.EQ.1)GO TO 150
IDIM2=MAXGEL
C
C calc the consensus and add the unused data if required
C save the lengths of the unused data in iladd, iradd
C (we dont use them here!)
C
CALL FILLI(ILADD,NCONTS,0)
CALL FILLI(IRADD,NCONTS,0)
JOB = 0
CALL JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM,JOB,KDUMM,KDUMM,KDUMM,KDUMM,
+TEMP3,
+ECHRSZ,MAXGL2,KBOUT,IDEV2,IFAIL,MAXGEL,IDM,PERCD,SEQ3,
+ILADD,IRADD,MAXCON,KDUMM,IWING,NBAD)
IF(IFAIL.NE.0) GO TO 400
ANS = 1
CALL RADION('Select output format',PROMPT,2,ANS,
+IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF (ANS.LT.1) GO TO 400
IF(ANS.EQ.1) THEN
CALL FMTDK(IDEV,SEQ1,IDIM)
ELSE
CALL WRITCF(IDEV,SEQ1,IDIM,NAMPRO,KBOUT,IOK)
END IF
RETURN
150 CONTINUE
CALL GETLN3(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+LINCON,LLINO,NULGEL,IERR,IDBSIZ,KBIN,KBOUT,IDEV3,
+'Contig identifier',
+IHELPS,IHELPE,FILEH,IDEVH)
IF(IERR.NE.0)GO TO 400
CALL GETREG(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+1,RELPG(LINCON),LREG,RREG,LINCON,LLINO,IDBSIZ,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IERR)
IF(IERR.NE.0)GO TO 400
IDIM2=RREG-LREG+1
IF((IDIM+20+IDIM2).GT.MAXSEQ)THEN
CALL ERROM(KBOUT,'Maximum consensus length exceeded')
CLOSE(UNIT=IDEV)
RETURN
END IF
JOB = 1
JCON = 1
CALL JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+ SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM,JOB,LLINO,LINCON,LREG,RREG,
+ TEMP3,
+ ECHRSZ,MAXGL2,KBOUT,IDEV2,IFAIL,MAXGEL,IDM,PERCD,SEQ3,
+ ILADD,IRADD,MAXCON,JCON,IWING,NBAD)
IF (IFAIL.NE.0) GO TO 400
300 CONTINUE
CALL YESNO(ANS,'Select another contig',
+IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(ANS.LT.0) GO TO 400
IF(ANS.EQ.0) GO TO 150
ANS = 1
CALL RADION('Select output format',PROMPT,2,ANS,
+IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF (ANS.LT.1) GO TO 400
IF(ANS.EQ.1) THEN
CALL FMTDK(IDEV,SEQ1,IDIM)
ELSE
CALL WRITCF(IDEV,SEQ1,IDIM,NAMPRO,KBOUT,IOK)
END IF
RETURN
400 CONTINUE
CLOSE(UNIT=IDEV)
END
C SUBROUTINE TO ENTER NEW GEL SEQUENCES INTO DATA BASE.
C IT READS IN AN ARCHIVE VERSION AND WRITES OUT A WORKING VERSION.
C IT ALSO SETS UP ANY RELATIONSHIPS WITH OTHER DATA IN THE DATABASE
C BOTH BY POSITION IN A CONTIG AND POINTERS TO LEFT AND RIGHT
C NEIGHBOURS.
SUBROUTINE AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+GEL,NAMARC,X,ITYPE,ISENSE,SEQC2,ITOTPC,
+IDIM,IDC,NCONTC,LINCON,IFAIL,IDBSIZ,KBOUT,IDEVR,IDEVW,IDEVN,
+IDEVT,IDEVC,IDEVG,MAXGEL)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),X,Y
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL),NAMARC*(*)
CHARACTER SEQC2(IDC)
CHARACTER NAMARK*16
C WRITE(*,*)'X,ITYPE,ISENSE,IDIM,IDC'
C WRITE(*,*)X,ITYPE,ISENSE,IDIM,IDC
C SET FAIL FLAG
IFAIL=0
C WRITE(KBOUT,1000)
C1000 FORMAT(' TRYING TO ENTER NEW GEL READING INTO DATABASE')
C IS THERE SPACE?
IF((IDBSIZ-(NGELS+NCONTS)).GT.2)GO TO 5
C FULL
WRITE(KBOUT,1999)IDBSIZ
1999 FORMAT(' Database full, current size=',I6,' Extend with copy')
IFAIL=7
RETURN
5 CONTINUE
C NEED TO CHECK TO SEE IF GEL ALREADY IN DB
C LOOK THRU ARC FILE
DO 10 J=1,NGELS
CALL READN(IDEVN,J,NAMARK)
IF(NAMARK.NE.NAMARC(1:16))GO TO 10
C FOUND
WRITE(KBOUT,1013)J
1013 FORMAT(' New gel already in database with number',I6,
+' Entry aborted')
IFAIL=6
RETURN
10 CONTINUE
C INCREMENT NUMBER OF GELS
NGELS=NGELS+1
C SET LENGTH THIS GEL
LNGTHG(NGELS)=IDIM*ISENSE
C WRITE NAME OF ARCHIVE TO LIST OF ARCHIVES
C NAMPRO,ARC
NAMARK=NAMARC(1:16)
CALL WRITEN(IDEVN,NGELS,NAMARK)
WRITE(KBOUT,1003)NGELS
1003 FORMAT(' This gel reading has been given the number ',I6)
C WRITE GEL TO WORKING VERSION
CALL WRITEW(IDEVW,NGELS,GEL,MAXGEL)
IF(IDEVT.GT.0) CALL ENTRD(IDEVG,IDEVT,IDEVC,NAMARC,NGELS,IOK)
C CREATE TAGS FOR THIS NASTY
CALL TAGGEL(NGELS,LNGTHG(NGELS),GEL)
C SET UP RELATIONSHIPS
C DOES THIS GEL OVERLAP?
IF(ITYPE.NE.0)GO TO 100
C
C DOES NOT OVERLAP SO IT STARTS A CONTIG OF ITS OWN
C SET LEFT AND RIGHT POINTERS TO ZERO,RELPG TO 1
LNBR(NGELS)=0
RNBR(NGELS)=0
RELPG(NGELS)=1
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C
C SET CONTIG POINTERS AND GENERAL VALUES
C INCREMENT NUMBER OF CONTIGS
NCONTS=NCONTS+1
C POINTER TO THIS CONTIG
N=IDBSIZ-NCONTS
C POINTER TO LEFT GEL THIS CONTIG
LNBR(N)=NGELS
C POINTER TO RIGHT GEL THIS CONTIG
RNBR(N)=NGELS
C LENGTH OF CONTIG
RELPG(N)=IDIM
C WRITE CONTIG DESCRIPTOR
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
C WRITE DB DESCRIPTOR
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
RETURN
C
100 CONTINUE
C
C
C DOES OVERLAP
150 CONTINUE
C
C LEFT END OR RIGHT OVERLAP?
IF(ITYPE.EQ.1)GO TO 400
C RIGHT END OR INTERNAL OVERLAP
C
160 CONTINUE
C NEED TO SEARCH THRU THIS CONTIG TO FIND LEFT AND RIGHT
C NEIGHBOURS FOR THIS NEW GEL
C LINE NUMBER OF LEFT END OF CONTIG
N=NCONTC
C LOOK THRU UNTIL CURRENT IS >= THEN IT MUST BE THE PREVIOUS ONE
200 CONTINUE
IF(RELPG(N).GT.X)GO TO 250
C IS THIS THE LAST GEL IN CONTIG?
IF(RNBR(N).EQ.0)GO TO 350
C NO SO LOOK AT NEXT
N=RNBR(N)
GO TO 200
250 CONTINUE
C GEL LIES BETWEEN N AND LNBR(N)
C NEED TO EDIT DB HERE
IF(ITOTPC.GT.0)CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
1NGELS,NCONTS,
2GEL,LINCON,X,SEQC2,ITOTPC,IDC,IDBSIZ,KBOUT,IDEVR,IDEVW,
+MAXGEL)
C
C
C SET POINTERS IN NEW GEL
LNBR(NGELS)=LNBR(N)
RNBR(NGELS)=N
RELPG(NGELS)=X
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C SET POINTERS IN LEFT AND RIGHT NEIGHBOURS
K=LNBR(N)
RNBR(K)=NGELS
C RNBR(LNBR(N))=NGELS
C WRITE LEFT AND RIGHT NEIGHBOURS
CALL WRITER(IDEVR,K,RELPG(K),LNGTHG(K),
+LNBR(K),RNBR(K))
LNBR(N)=NGELS
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
C WRITE NGELS NCONTS
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
C HAVE WE INCREASED LENGTH OF CONTIG?
C ITS LINE NUMBER IS LINCON
C NEED TO UPDATE IDIM IN CASE OF EDITS
IDIM=ABS(LNGTHG(NGELS))
Y=X+IDIM-1
IF(Y.LE.RELPG(LINCON))RETURN
RELPG(LINCON)=Y
C WRITE NEW CONTIG LINE
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
RETURN
350 CONTINUE
C MUST BE A RIGHT END OVERLAP
C NEED TO EDIT DB HERE
IF(ITOTPC.GT.0)CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
1NGELS,NCONTS,
2GEL,LINCON,X,SEQC2,ITOTPC,IDC,IDBSIZ,KBOUT,IDEVR,IDEVW,
+MAXGEL)
C
C
C SET POINTERS FOR NEW GEL
LNBR(NGELS)=N
RNBR(NGELS)=0
RELPG(NGELS)=X
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C OLD RIGHT END
RNBR(N)=NGELS
C WRITE NEW RIGHT LINE
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
C RESET RIGHT NAME IN CONTIG
C ITS LINE NUMBER IS LINCON
RNBR(LINCON)=NGELS
C HAVE WE INCREASED LENGTH OF CONTIG?
C NEED TO UPDATE LENGTH OF GEL IN CASE OF EDITS
IDIM=ABS(LNGTHG(NGELS))
Y=X+IDIM-1
RELPG(LINCON)=MAX(RELPG(LINCON),Y)
C WRITE HERE
C WRITE CONTIG DESCRIPTOR
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
RETURN
C
400 CONTINUE
C
C ADDING TO LEFT END
410 CONTINUE
C NEED TO EDIT DB HERE
IF(ITOTPC.GT.0)CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
1NGELS,NCONTS,
2GEL,LINCON,1,SEQC2,ITOTPC,IDC,IDBSIZ,KBOUT,IDEVR,IDEVW,
+MAXGEL)
C
420 CONTINUE
C SET POINTERS IN NEW GEL
RELPG(NGELS)=1
RNBR(NGELS)=NCONTC
LNBR(NGELS)=0
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C SET POINTERS IN OLD LEFT END
LNBR(NCONTC)=NGELS
RELPG(NCONTC)=X
C WRITE NEW LEFT END
CALL WRITER(IDEVR,NCONTC,RELPG(NCONTC),LNGTHG(NCONTC),
+LNBR(NCONTC),RNBR(NCONTC))
C NEW LENGTH OF CONTIG
RELPG(LINCON)=RELPG(LINCON)+X-1
C MAY HAVE JUST ADDED A GEL LONGER THAN CONTIG
IDIM=ABS(LNGTHG(NGELS))
Y=IDIM
IF(Y.GT.RELPG(LINCON))RELPG(LINCON)=Y
C NEW NAME OF LEFT END OF CONTIG
LNBR(LINCON)=NGELS
C WRITE CONTIG DESCRIPTOR
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
C NOW GO THRU AND CHANGE ALL RELATIVE POSITIONS
N=NCONTC
440 CONTINUE
IF(RNBR(N).EQ.0)RETURN
N=RNBR(N)
RELPG(N)=RELPG(N)+X-1
C WRITE NEW LINE
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
GO TO 440
END
SUBROUTINE COPYTG(IDEVT,IDEV,IOK,IDBSIZ,NEWSIZ,NGELS)
C Read tag details
IDIFF = NEWSIZ - IDBSIZ
CALL READTG(IDEVT,IDBSIZ,ICNT,LLEN,LCOM,LTYPE,NEXT)
IF (NEXT.NE.0) NEXT = NEXT + IDIFF
CALL WRITTG(IDEV,NEWSIZ,ICNT+IDIFF,LLEN,LCOM,LTYPE,NEXT)
C Copy headers for each gels
DO 10 I = 1,NGELS
CALL READTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF (NEXT.NE.0) NEXT = NEXT + IDIFF
CALL WRITTG(IDEV,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
10 CONTINUE
C Copy rest of tags
DO 20 I = IDBSIZ+1, ICNT
CALL READTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF (NEXT.NE.0) NEXT = NEXT + IDIFF
CALL WRITTG(IDEV,I+IDIFF,LPOS,LLEN,LCOM,LTYPE,NEXT)
20 CONTINUE
IOK = 0
END
SUBROUTINE COPYCC(IDEVC,IDEV,IOK)
C COMMENT_LENGTH
CHARACTER NOTE*40
CALL READCC(IDEVC,1,ICNT,NEXT,NOTE)
CALL WRITCC(IDEV,1,ICNT,NEXT,NOTE)
DO 10 I = 2,ICNT
CALL READCC(IDEVC,I,ICNT,NEXT,NOTE)
CALL WRITCC(IDEV,I,ICNT,NEXT,NOTE)
10 CONTINUE
IOK = 0
END
SUBROUTINE DBAUTO(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
+NGELS,NCONTS,MAXGEL,
+TEMP3,WORDP,WORDN,LPOWRC,POSNS,GELN,
+SEQ1,MAXSEQ,SEQ2,SEQ3,SEQ4,SEQ5,SEQC2,SEQG2,MATCH,
+MAXGLM,MAXGL2,CHRSIZ,ECHRSZ,LENGTH,
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,CONST,
+KBIN,KBOUT,IDEV1,IDEV2,IDEV3,IDEV4,IDEV7,IDEV8,IDEV,IDEVT,IDEVC,
+IHELPS,IHELPE,HELPF,IDEVH,NAMARC,NAMPRO,FILE,
+PERCD,IOPEN,IDM,SEQG3,SEQC3,IOK)
INTEGER CHRSIZ,ECHRSZ
INTEGER RELPG(MAXDB),PL(2),PR(2),RMOST
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
INTEGER JOINT(2),ITOTPC(2),ITOTPG(2),IDIM22(2),IDOUT(2)
INTEGER LINCON(2),LLINO(2),ITYPE(2),IFAIL(2)
INTEGER ILEFTS(2),ILC(2),IPOSC(2),IPOSG(2),ISENSE(2)
INTEGER LREG,RREG,X,ANSJOK
INTEGER TEMP3(ECHRSZ,MAXGL2),CONST(LENGTH)
INTEGER POSNS(MAXSEQ),WORDP(LPOWRC),WORDN(LPOWRC),GELN(MAXGLM)
INTEGER CENDS(MAXCON),NENDS(MAXCON)
CHARACTER SEQ3(MAXGLM),SEQC2(MAXGLM,2),SEQG2(MAXGLM,2)
CHARACTER SEQ1(MAXSEQ),SEQ2(MAXGLM),MATCH(MAXGLM),SEQ4(MAXGLM)
INTEGER SAV1(MAXSAV),SAV2(MAXSAV),SAV3(MAXSAV),CSTART
CHARACTER NAMARC*(*),NAMPRO*(*),FILE*(*)
CHARACTER GET,SEQ5(MAXGLM),HELPF*(*),SEQG3(MAXGLM),SEQC3(MAXGLM)
PARAMETER (MAXPRM = 32)
CHARACTER PROMPT(3)*(MAXPRM)
REAL PERMIS(2)
INTEGER GNFFOF
EXTERNAL GNFFOF
SAVE GET
DATA GET/'>'/
WRITE(KBOUT,*)' Automatic sequence assembler'
C
C set flag for saving alignment scores
C
IREPSC = 1
ICRAP = 1
IFAIL(1) = 0
IEMPTY=0
IF(NGELS.LT.1)IEMPTY=1
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+TEMP3,IERR,KBOUT)
IF(IERR.GT.1) RETURN
CALL YESNO(IOKENT,'Permit entry',
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(IOKENT.LT.0) RETURN
CALL YESNO(ISHOW,'Hide alignments',
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(ISHOW.LT.0) RETURN
CALL YESNO(INF,'Use file of file names',
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(INF.LT.0) RETURN
IF(INF.EQ.0) THEN
FILE = ' '
CALL OPENF1(IDEV7,FILE,0,IOK,KBIN,KBOUT,
+ 'File of gel reading names',
+ IHELPS,IHELPE,HELPF,IDEVH)
IF(IOK.NE.0) RETURN
END IF
IF(IOKENT.EQ.0) THEN
FILE = ' '
CALL OPENF1(IDEV8,FILE,1,IOK,KBIN,KBOUT,
+ 'File for names of failures',
+ IHELPS,IHELPE,HELPF,IDEVH)
IF(IOK.NE.0) RETURN
ELSE
CALL YESNO(IREPSC,'Save alignment scores in a file',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(IREPSC.LT.0) RETURN
IF(IREPSC.EQ.0) THEN
FILE = ' '
CALL OPENF1(IDEV8,FILE,1,IOK,KBIN,KBOUT,
+ 'File for names and scores',
+ IHELPS,IHELPE,HELPF,IDEVH)
IF(IOK.NE.0) RETURN
CALL YESNO(ICRAP,'Use poor data',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(ICRAP.LT.0) RETURN
END IF
END IF
PROMPT(1) = 'Perform normal shotgun assembly'
PROMPT(2) = 'Put all sequences in one contig'
PROMPT(3) = 'Put all sequences in new contigs'
IOPT = 1
CALL RADION('Select entry mode',PROMPT,3,IOPT,
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(IOPT.LT.1) RETURN
IF(IOPT.EQ.1) THEN
C parameters for normal assembly
ANSJOK = 0
CALL YESNO(ANSJOK,'Permit joins',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(ANSJOK.LT.0) RETURN
MN = LENGTH*2
MX = MAXGLM + 1
MINMAT = MAX(15,MN)
CALL GETINT(MN,MX,MINMAT,
+ 'Minimum initial match',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MINMAT = IVAL
MINSLI = 3
MN = 0
MX = 25
MAXPG = 8
CALL GETINT(MN,MX,MAXPG,
+ 'Maximum pads per gel',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXPG = IVAL
MN = 0
MX = 25
MAXPC = 8
CALL GETINT(MN,MX,MAXPC,
+ 'Maximum pads per gel in contig',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXPC = IVAL
C IF((IOKENT.EQ.0).OR.(IREPSC.EQ.0)) THEN
RMN = 0.
RMX = 100.
PERMAX = 8.
CALL GETRL(RMN,RMX,PERMAX,
+ 'Maximum percent mismatch after alignment',
+ VAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
PERMAX = VAL
C END IF
IDIM1=0
MAXOVR=MAXGEL-3*MAX(MAXPC,MAXPG)
JGEL = 0
JNGEL = 0
JNJOIN = 0
JOINF = 0
IMATC = 0
IF(IEMPTY.EQ.0) THEN
JOB = 0
CALL ACONSN(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+ SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,JOB,KDUMM,KDUMM,KDUMM,TEMP3,
+ ECHRSZ,MAXGL2,KBOUT,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0) THEN
CALL ERROM(KBOUT,'Error calculating consensus')
GO TO 900
END IF
END IF
C
C init hashing constants
C
CALL INITE(CONST,CSTART,LENGTH)
END IF
C
C set intitial values for contig count and number of readings
C just to get thru the first consensus calc
NGELSL = NGELS + 2
NCONTL = NCONTS +1
C
C
C MAIN LOOP
C
C
1 CONTINUE
C IF(IDIM1.GT.0)CALL FMTDB(SEQ1,IDIM1,1,IDIM1,60,IDEV)
C
C
IDIM2=MAXGEL
IF(INF.EQ.1) THEN
3 CONTINUE
MN = 0
CALL GTSTR('Gel reading name',' ',NAMARC,MN,KBOUT,KBIN,INFLAG)
IF(INFLAG.EQ.3) RETURN
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 3
END IF
ELSE
IOK = GNFFOF(IDEV7,NAMARC)
IF(IOK.EQ.1) GO TO 900
IF(IOK.NE.0) GO TO 1
END IF
DO 77 MM=1,80
MATCH(MM)=GET
77 CONTINUE
WRITE(IDEV,1077)(MATCH(KK),KK=1,79)
1077 FORMAT(' ',79A1)
JGEL = JGEL + 1
WRITE(IDEV,*)'Processing',JGEL,' in batch'
1007 FORMAT(' Gel reading name=',A)
WRITE(IDEV,1007)NAMARC
CALL OPENRS(IDEV4,NAMARC,IOK,LRECL,2)
IF(IOK.NE.0)THEN
C IF(INF.EQ.1) RETURN
CALL AERROR(IDEV,IDEV8,NAMARC,0)
GO TO 1
END IF
CALL ARRFIN(IDEV4,SEQ2,IDIM2,KBOUT,ICRAP)
CLOSE(UNIT=IDEV4)
WRITE(IDEV,1800)IDIM2
1800 FORMAT(' Gel reading length=',I6)
C
C
C
IF(IOPT.NE.1) THEN
CALL DBAUTP(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,MAXDB,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL,IMATC,IEMPTY,IOPT)
IF(IFAIL(1).NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,0)
ELSE
JNGEL = JNGEL + 1
END IF
GO TO 1
END IF
IF(IDIM2.LT.MINMAT)THEN
CALL AERROR(IDEV,IDEV8,NAMARC,1)
GO TO 1
END IF
CALL SQCOPY(SEQ2,SEQ3,IDIM2)
IFCOMP=0
IMATC=0
JOBC = 2
IF ((NGELSL.LT.NGELS).AND.(NCONTL.LT.NCONTS)) THEN
JOBC = 1
ELSE IF (NGELSL.EQ.NGELS) THEN
JOBC = 0
END IF
NGELSL = NGELS
NCONTL = NCONTS
IF(IEMPTY.EQ.0)
+CALL AUTOCN(SEQ1,IDIM1,SEQ2,IDIM2,ILEFTS,ILC,IPOSC,
+IPOSG,ISENSE,LLINO,IMATC,IFCOMP,MINMAT,POSNS,WORDP,WORDN,
+CONST,LENGTH,LPOWRC,IDEV,MATCH,MAXGEL,MAXGLM,SEQ5,GELN,
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,
+SEQG2,SEQC2,SEQ4,IDOUT,IDIM22,ITOTPG,ITOTPC,JOINT,IFAIL,
+ITYPE,MAXPC,MAXPG,PERMAX,MINSLI,SEQG3,SEQC3,KFAIL,CSTART,
+JOBC,PERMIS,LENO,ISHOW)
IF(IREPSC.EQ.0) THEN
IF(IFCOMP.NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,2)
GO TO 1
END IF
IF(IMATC.GT.0) THEN
WRITE(IDEV8,1022)NAMARC,PERMIS(1),IDIM2,LENO
ELSE
PERMIS(1) = 0.
LENO = 0
WRITE(IDEV8,1022)NAMARC,PERMIS(1),IDIM2,LENO
END IF
END IF
1022 FORMAT(' ',A,F5.1,2I6)
IF(IOKENT.NE.0) GO TO 1
C THIS RETURNS THE FOLLOWING:
C ILEFTS POSITION IN CONSENSUS OF LEFT END OF MATCHING CONTIGS
C ILC LENGTHS OF MATCHING CONTIGS
C IPOSC POSITION OF MATCH RELATIVE TO CONTIG
C IPOSG POSITION OF MATCH RELATIVE TO NEW GEL
C ISENSE SENSE OF NEW GEL
C LLINO LEFT GEL NUMBER IN MATCHING CONTIGS
C IMATC THE NUMBER OF MATCHING CONTIGS (>2 IS ERROR!)
C IFCOMP ERROR FLAG FOR COMPARISON (COMPARISON ARRAYS OVERFLOWED)
IF(IFCOMP.NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,2)
GO TO 1
END IF
CALL SQCOPY(SEQ3,SEQ2,IDIM2)
IF(IMATC.EQ.0) THEN
C
C NO OVERLAP NEW CONTIG
C
C ITYPE 0 = NO OVERLAP
C ISENSE 1 = SAME SENSE AS ARCHIVE
IF(IFAIL(1).NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,2)
GO TO 1
END IF
ITYPE(1)=0
ISENSE(1)=1
IDOUT(1)=MAXGEL
WRITE(IDEV,1015)
1015 FORMAT(' New gel reading does not overlap: start a new contig')
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,X,ITYPE,ISENSE,SEQC2(1,1),ITOTPC(1),
+ IDIM2,IDOUT(1),LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL(1).NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,3)
GO TO 1
END IF
IEMPTY=0
IDIM1=IDIM1+1
IF((IDIM1+19+IDIM2).GT.MAXSEQ)THEN
WRITE(IDEV,1021)MAXSEQ
1021 FORMAT(' Database maximum consensus length (',I6,') exceeded')
GO TO 900
END IF
CALL ADDTIT(SEQ1(IDIM1),NAMPRO,NGELS,IDIM1)
CALL MSTLKL(SEQ2,IDIM2)
CALL SQCOPY(SEQ2,SEQ1(IDIM1),IDIM2)
IDIM1=IDIM1+IDIM2-1
JNGEL = JNGEL + 1
GO TO 1
END IF
C
C
C OVERLAP SO TRY TO ALIGN THE SEQUENCES
C
C
DO 100 I=1,IMATC
N=IDBSIZ-NCONTS
DO 99 J=N,IDBSIZ-1
IF(LNBR(J).NE.LLINO(I))GO TO 99
LINCON(I)=J
GO TO 100
99 CONTINUE
WRITE(IDEV,10077)LLINO(I)
10077 FORMAT(' Contig line for contig',I6,' not found!')
GO TO 900
100 CONTINUE
C
IF (IMATC.EQ.1) THEN
C
C
C SINGLE OVERLAP
C
C
C
WRITE(IDEV,1014)LLINO(1)
1014 FORMAT(' New gel reading overlaps contig',I6)
IF(ITOTPG(1).GT.0) CALL CCTA(SEQG2(1,1),IDIM22(1))
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQG2(1,1),NAMARC,JOINT(1),ITYPE(1),ISENSE(1),
+ SEQC2(1,1),
+ ITOTPC(1),IDIM22(1),IDOUT(1),LLINO(1),LINCON(1),
+ IFAIL(1),IDBSIZ,IDEV,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL(1).NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,3)
GO TO 1
END IF
JNGEL = JNGEL + 1
CALL UPDCON(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,NCONTS,
+ SEQ1,MAXSEQ,IDIM1,ILEFTS(1),ILC(1),LINCON(1),NAMPRO,SEQ2,TEMP3,
+ ECHRSZ,MAXGL2,KBOUT,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0) THEN
CALL ERROM(KBOUT,'Error calculating consensus')
GO TO 900
END IF
IF(KFAIL.NE.0) THEN
C CALL AERROR(IDEV,IDEV8,NAMARC,4)
END IF
GO TO 1
END IF
C
C
C DOUBLE OVERLAP
C
C
WRITE(IDEV,1013)LLINO
1013 FORMAT(' Overlap between contigs',I6,' and',I6)
IF(ANSJOK.NE.0) GO TO 1
IF(LLINO(1).EQ.LLINO(2))THEN
WRITE(IDEV,*)' Trying to form loop in contig',LLINO(1)
WRITE(IDEV,*)' Gel not entered'
CALL AERROR(IDEV,IDEV8,NAMARC,3)
GO TO 1
END IF
CALL AJOIN3(RELPG,IDBSIZ,LINCON,ITYPE,ISENSE,JOINT,
+IDIM22,KLASS,IOVER,IDEV,PL,PR)
IF(IOVER.GT.MAXOVR)THEN
WRITE(IDEV,*)' Overlap too large: entry only'
C
C cannot align the two contigs, so try to enter the reading into one of them
C
IFAIL(2)=1
IGOOD=0
IF(IFAIL(1).EQ.0)IGOOD=1
IF(IFAIL(2).EQ.0)IGOOD=2
IF(IGOOD.EQ.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,2)
JOINF = JOINF + 1
GO TO 1
END IF
IF(ITOTPG(IGOOD).GT.0) CALL CCTA(SEQG2(1,IGOOD),IDIM22(IGOOD))
WRITE(IDEV,1012)LLINO(IGOOD)
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQG2(1,IGOOD),NAMARC,JOINT(IGOOD),ITYPE(IGOOD),
+ ISENSE(IGOOD),SEQC2(1,IGOOD),ITOTPC(IGOOD),
+ IDIM22(IGOOD),IDOUT(IGOOD),LLINO(IGOOD),LINCON(IGOOD),
+ IFAIL(IGOOD),IDBSIZ,IDEV,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,
+ MAXGEL)
IF(IFAIL(IGOOD).NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,3)
JOINF = JOINF + 1
GO TO 1
END IF
JNGEL = JNGEL + 1
CALL UPDCON(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,NCONTS,
+ SEQ1,MAXSEQ,IDIM1,ILEFTS(IGOOD),ILC(IGOOD),LINCON(IGOOD),
+ NAMPRO,SEQ2,TEMP3,
+ ECHRSZ,MAXGL2,KBOUT,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0) THEN
CALL ERROM(KBOUT,'Error calculating consensus')
GO TO 900
END IF
WRITE(IDEV,1020)LLINO,LLINO(IGOOD)
1020 FORMAT(' Could not join contigs',I4,' and',I4,' but the gel',
+ ' has been entered into contig',I4,/,
+ ' If required do the join manually.')
JOINF = JOINF + 1
GO TO 1
END IF
C WHICH CONTIG IS LEFTMOST?
LMOST=1
RMOST=2
IF(PL(1).GT.PL(2))THEN
LMOST=2
RMOST=1
END IF
C SAVE LENGTH OF RMOST CONTIG FOR DELETION STEP LATER
ILCR=ILC(RMOST)
IF(ITOTPG(LMOST).GT.0) CALL CCTA(SEQG2(1,LMOST),IDIM22(LMOST))
WRITE(IDEV,1012)LLINO(LMOST)
1012 FORMAT(' Entering the new gel reading into contig',I6)
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQG2(1,LMOST),NAMARC,JOINT(LMOST),ITYPE(LMOST),
+ISENSE(LMOST),SEQC2(1,LMOST),ITOTPC(LMOST),
+IDIM22(LMOST),IDOUT(LMOST),LLINO(LMOST),LINCON(LMOST),
+IFAIL(LMOST),IDBSIZ,IDEV,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,
+MAXGEL)
IF(IFAIL(LMOST).NE.0) THEN
CALL AERROR(IDEV,IDEV8,NAMARC,3)
JOINF = JOINF + 1
GO TO 1
END IF
JNGEL = JNGEL + 1
CALL UPDCON(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,NCONTS,
+ SEQ1,MAXSEQ,IDIM1,ILEFTS(LMOST),ILC(LMOST),LINCON(LMOST),
+ NAMPRO,SEQ2,TEMP3,
+ ECHRSZ,MAXGL2,KBOUT,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0) THEN
CALL ERROM(KBOUT,'Error calculating consensus')
GO TO 900
END IF
IF(ITYPE(LMOST).EQ.1)LLINO(LMOST)=NGELS
IF(ILEFTS(LMOST).LT.ILEFTS(RMOST))THEN
ILEFTS(RMOST)=ILEFTS(RMOST) +
+ (RELPG(LINCON(LMOST)) - ILC(LMOST))
END IF
ILC(LMOST) = RELPG(LINCON(LMOST))
DO 500 I=1,2
IF(ISENSE(I).EQ.-1)THEN
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON(I),
+ LLINO(I),SEQ2,IDBSIZ,IDEV,IDEV1,IDEV2,MAXGEL)
CALL SQREV(SEQ1(ILEFTS(I)),ILC(I))
CALL SQCOM(SEQ1(ILEFTS(I)),ILC(I))
KT=IDIM1
CALL ADDTIT(SEQ1((ILEFTS(I)-20)),NAMPRO,LNBR(LINCON(I)),KT)
END IF
500 CONTINUE
C NEED TO KNOW POSITION OF OVERLAP RELATIVE TO CONTIG, TO CONSENSUS
C WHICH BITS TO SEND TO ALIGNMENT ROUTINES
C SET UP FOR ALINE (NOTE RMOST IS EQUIVALENT TO THE GEL READING AND
C SO IS SLID ALONG THE LMOST CONTIG. THE SECTION SENT TO ALINE MUST
C BE OF LENGTH < MAXGEL-2*MAX(MAXPC,MAXPG)
C IT MUST START AT POSITION 1 IN THE RMOST CONTIG AND EXTEND
IPOSC(LMOST)=PL(RMOST)+RELPG(NGELS)-1
ILCT = RELPG(LINCON(LMOST)) - RELPG(NGELS) - PL(RMOST) + 2
ILC(RMOST)=MIN(ILCT,ILC(RMOST))
IPOSC(RMOST)=1
IDOUT(LMOST)=MAXGEL
IDOUT(RMOST)=MAXGEL
IDSAV=MAXSAV
C ON INPUT TO ALINE ILC(RMOST) CONTAINS THE OVERLAP LENGTH
C ON OUTPUT IT CONTAINS THE LENGTH OF THE ALIGNED SECTION (IE INCLUDING
C PADS)
WRITE(IDEV,1009)
1009 FORMAT(' Trying to align the two contigs')
CALL ALINE(SEQ1(ILEFTS(LMOST)),SEQ1(ILEFTS(RMOST)),
+SEQC2(1,RMOST),SEQC2(1,LMOST),SAV1,SAV2,SAV3,IDSAV,
+ILC(LMOST),ILC(RMOST),IDOUT(LMOST),IPOSC(LMOST),IPOSC(RMOST),
+MINSLI,JOINT(LMOST),ITOTPC(LMOST),ITOTPC(RMOST),IFAIL(1),
+ITYPE(1),MAXPC,MAXPC,PERMAX,IDEV,SEQ4,MAXGEL,Z,LENO,ISHOW)
C SEQC2(1,LMOST) NOW CONTAINS THE ALIGNED SECTION OF THE LMOST CONTIG
C SEQC2(1,RMOST) NOW CONTAINS THE ALIGNED SECTION OF THE RMOST CONTIG
C ILC(RMOST) IS NOW THE LENGTH OF ALIGNED SECTION OF THE RMOST CONTIG
C IDOUT(LMOST) IS NOW THE LENGTH OF ALIGNED SECTION OF THE LMOST CONTIG
C JOINT(LMOST) IS THE POSITION OF THE JOIN RLETIVE TO THE LMOST CONTIG
C ITYPE IS TYPE OF OVERLAP (-1 = RIGHT END OR INTERNAL, 1 = LEFT END)
C NB SHOULD ALWAYS BE -1
C IF THIS HAS BEEN DONE OK WE CAN EDIT THE TWO CONTIGS THEN JOIN
IF(IFAIL(1).NE.0)THEN
WRITE(IDEV,*)' Failed to align the two overlapping contigs'
C CALL AERROR(IDEV,IDEV8,NAMARC,4)
JOINF = JOINF + 1
GO TO 1
END IF
IF(ITOTPC(LMOST).GT.0)THEN
WRITE(IDEV,1017)LLINO(LMOST)
1017 FORMAT(' Editing contig',I6)
CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
+ NGELS,NCONTS,SEQ3,LINCON(LMOST),JOINT(LMOST),SEQC2(1,LMOST),
+ ITOTPC(LMOST),IDOUT(LMOST),IDBSIZ,IDEV,IDEV1,IDEV2,
+ MAXGEL)
END IF
JOINT(RMOST)=1
IDOUT(RMOST)=ILC(RMOST)
IF(ITOTPC(RMOST).GT.0)THEN
WRITE(IDEV,1017)LLINO(RMOST)
CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
+ NGELS,NCONTS,SEQ3,LINCON(RMOST),JOINT(RMOST),SEQC2(1,RMOST),
+ ITOTPC(RMOST),IDOUT(RMOST),IDBSIZ,IDEV,IDEV1,IDEV2,
+ MAXGEL)
END IF
ILC(RMOST)=ILCR
LTL=LNBR(LINCON(LMOST))
LTR=LNBR(LINCON(RMOST))
WRITE(IDEV,1018)LNBR(LINCON(LMOST)),LNBR(LINCON(RMOST))
1018 FORMAT(' Completing the join between contigs',I6,' and',I6)
CALL AJOIN2(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+JOINT(LMOST),LTL,LTR,LINCON(LMOST),LINCON(RMOST),IDEV1)
LLINO(1)=LTL
IF(ILEFTS(LMOST).GT.ILEFTS(RMOST))THEN
CALL DELCON(SEQ1,ILEFTS(LMOST),ILC(LMOST),IDIM1)
CALL DELCON(SEQ1,ILEFTS(RMOST),ILC(RMOST),IDIM1)
END IF
IF(ILEFTS(RMOST).GE.ILEFTS(LMOST))THEN
CALL DELCON(SEQ1,ILEFTS(RMOST),ILC(RMOST),IDIM1)
CALL DELCON(SEQ1,ILEFTS(LMOST),ILC(LMOST),IDIM1)
END IF
LREG=1
RREG=JOINT(LMOST)
IGELC=LLINO(1)
JOB = 1
CALL ACONSN(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,JOB,IGELC,LREG,RREG,TEMP3,
+ECHRSZ,MAXGL2,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0) THEN
CALL ERROM(KBOUT,'Error calculating consensus')
GO TO 900
END IF
C CALL FMTDB(SEQ1,IDIM1,1,IDIM1,60,IDEV)
JNJOIN = JNJOIN + 1
IF(KFAIL.NE.0) THEN
C CALL AERROR(IDEV,IDEV8,NAMARC,4)
C JOINF = JOINF + 1
END IF
GO TO 1
900 CONTINUE
C CALL FMTDB(SEQ1,IDIM1,1,IDIM1,60,IDEV)
WRITE(KBOUT,*)'Batch finished'
WRITE(KBOUT,*)JGEL,' sequences processed'
WRITE(KBOUT,*)JNGEL,' sequences entered into database'
WRITE(KBOUT,*)JNJOIN,' joins made'
WRITE(KBOUT,*)JOINF, ' joins failed'
END
SUBROUTINE DBAUTP(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,MAXDB,IDEV,
+IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL,IMATC,IEMPTY,IOPT)
INTEGER RELPG(MAXDB)
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
CHARACTER SEQ2(MAXGEL),SEQC2(MAXGEL)
CHARACTER NAMARC*(*)
C deals with entering all readings into contig 1 (IOPT=2)
C or all readings into new contigs (IOPT=3)
IF(IOPT.EQ.2) THEN
IF(IMATC.EQ.0) THEN
ITYPE=0
ISENSE=1
IDOUT=MAXGEL
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL.NE.0) RETURN
IEMPTY=0
IMATC = 1
ELSE
ITYPE= - 1
ISENSE=1
JOINT = 1
LLINO = 1
LINCON = IDBSIZ - 1
ITOTPC = 0
IDOUT=MAXGEL
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVT,IDEV4,MAXGEL)
IF(IFAIL.NE.0) RETURN
END IF
ELSE IF(IOPT.EQ.3) THEN
ITYPE=0
ISENSE=1
IDOUT=MAXGEL
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL.NE.0) RETURN
END IF
END
SUBROUTINE DBCOPY(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,GEL,
+NAMPRO,IDEV,IDBSIZ,IERR,KBIN,KBOUT,IDEVR,IDEVW,IDEVN,
+IDEVT,IDEVC,
+IHELPS,IHELPE,FILEH,IDEVH,MAXGEL,MAXDB,IDM)
CHARACTER FILEH*(*)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER NAMPRO*(*),NAMARC*16,GEL(MAXGEL)
CHARACTER V2,V1,VIN
INTEGER IWORD,DELDB,ACTF
PARAMETER (IWORD=4)
PARAMETER (MAXPRM = 21)
CHARACTER PERR(2)*(MAXPRM)
EXTERNAL DELDB,ACTF
IERR=1
LL = INDEX(NAMPRO,'.')
C
C save incoming version
C
VIN = NAMPRO(LL+1:LL+1)
1 CONTINUE
L = 1
V1='1'
CALL GTSTR('Make version',V1,V2,L,KBOUT,KBIN,INFLAG)
CALL CCASE(V2,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 1
END IF
IF(L.LT.1) V2 = V1
C
C check if file is open
C
NAMPRO(LL+1:LL+1) = V2
LM1 = LL - 1
IOK = ACTF(1,NAMPRO,LM1,V2,KBOUT)
IF (IOK.NE.0) THEN
NAMPRO(LL+1:LL+1) = VIN
RETURN
END IF
MN = NGELS + NCONTS + 1
MX = MAXDB
NEWSIZ = IDBSIZ
CALL GETINT(MN,MX,NEWSIZ,
+'New database size',
+IVAL,KBIN,KBOUT,IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 40
CALL BUSY(KBOUT)
NEWSIZ = IVAL
C WHERE SHOULD CHARS BE CHANGED ?
LLL = INDEX(NAMPRO,'.') + 1
NAMPRO(LLL:)='RL'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,4,3)
IF(IOK.NE.0) THEN
C problem opening file
IF(IOK.EQ.2) THEN
CALL ERROM(KBOUT,'File already exists')
PERR(1) = 'Retype version number'
PERR(2) = 'Replace database'
IDO = 1
CALL RADION('Select action',PERR,2,IDO,
+ IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(IDO.LT.1) GO TO 40
IF(IDO.EQ.1) THEN
C
C close busy file (note we dont care what we send for job=2!!!)
C
NAMPRO(LL+1:LL+1) = V2
IOK = ACTF(2,NAMPRO,LLL,V2,KBOUT)
IF (IOK.NE.0) THEN
C should never get here
NAMPRO(LL+1:LL+1) = VIN
RETURN
END IF
GO TO 1
END IF
IF(IDO.EQ.2) THEN
IOK = DELDB(NAMPRO,V2,IDEV,MAXGEL)
IF(IOK.EQ.0) THEN
LLL = INDEX(NAMPRO,'.') + 1
NAMPRO(LLL:)='RL'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,4,3)
IF(IOK.EQ.0) GO TO 2
ELSE
CALL ERROM(KBOUT,'File delete failed')
END IF
END IF
END IF
GO TO 100
END IF
2 CONTINUE
CALL WRITER(IDEV,0,MAXDB,NEWSIZ,MAXGEL,IDM)
CALL WRITER(IDEV,NEWSIZ,NGELS,NCONTS,NGELS,NCONTS)
DO 10 I=1,NGELS
CALL WRITER(IDEV,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
10 CONTINUE
M=NEWSIZ-NCONTS
N=IDBSIZ-NCONTS
DO 15 I=N,IDBSIZ-1
CALL WRITER(IDEV,M,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
M=M+1
15 CONTINUE
CLOSE(UNIT=IDEV)
C DO SEQUENCES
NAMPRO(LLL:)='SQ'//V2
IREC=MAXGEL/IWORD
IF(MOD(MAXGEL,IWORD).NE.0)IREC=IREC+1
CALL OPENRS(IDEV,NAMPRO,IOK,IREC,3)
IF(IOK.NE.0)GO TO 100
DO 20 I=1,NGELS
CALL READW(IDEVW,I,GEL,MAXGEL)
CALL WRITEW(IDEV,I,GEL,MAXGEL)
20 CONTINUE
CLOSE(UNIT=IDEV)
C DO ARCHIVE NAMES
NAMPRO(LLL:)='AR'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,4,3)
IF(IOK.NE.0)GO TO 100
DO 30 I=1,NGELS
CALL READN(IDEVN,I,NAMARC)
CALL WRITEN(IDEV,I,NAMARC)
30 CONTINUE
CLOSE(UNIT=IDEV)
IF(IDEVT.GT.0.AND.IDEVC.GT.0) THEN
NAMPRO(LLL:)='TG'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,5,3)
IF(IOK.NE.0)GO TO 100
CALL COPYTG(IDEVT,IDEV,IOK,IDBSIZ,NEWSIZ,NGELS)
CLOSE(UNIT=IDEV)
NAMPRO(LLL:)='CC'//V2
C COMMENT_LENGTH: 11 = (40 + long)/long
CALL OPENRS(IDEV,NAMPRO,IOK,11,3)
IF(IOK.NE.0)GO TO 100
CALL COPYCC(IDEVC,IDEV,IOK)
CLOSE(UNIT=IDEV)
ENDIF
IERR=0
40 CONTINUE
C
C close busy file (note we dont care what we send for job=2!!!)
C
LL = INDEX(NAMPRO,'.')
NAMPRO(LL+1:LL+1) = V2
IOK = ACTF(2,NAMPRO,LL,V2,KBOUT)
NAMPRO(LL+1:LL+1) = VIN
RETURN
100 CONTINUE
WRITE(KBOUT,9999)
9999 FORMAT(' Error opening new database, copy aborted')
C
C close busy file
C
LL = INDEX(NAMPRO,'.')
NAMPRO(LL+1:LL+1) = V2
IOK = ACTF(2,NAMPRO,LL,V2,KBOUT)
NAMPRO(LL+1:LL+1) = VIN
END
INTEGER FUNCTION DELDB(NAMPRO,VERSN,IDEV,MAXGEL)
CHARACTER NAMPRO*(*),VERSN
INTEGER DELF
EXTERNAL DELF
C
C delete an xdap database (bap): names are 16 characters!
C
C assume relationships are 4 words, names are 4 and seqs are maxgel
C all recls in BYTES
C
DELDB = 1
LLL = INDEX(NAMPRO,'.') + 1
NAMPRO(LLL:)='RL'//VERSN
IF(DELF(NAMPRO,IDEV,16,4).NE.0) RETURN
NAMPRO(LLL:)='AR'//VERSN
IF(DELF(NAMPRO,IDEV,16,4).NE.0) RETURN
NAMPRO(LLL:)='SQ'//VERSN
IF(DELF(NAMPRO,IDEV,MAXGEL,4).NE.0) RETURN
NAMPRO(LLL:)='CC'//VERSN
C COMMENT_LENGTH: 11 = (40 + long)/long
IF(DELF(NAMPRO,IDEV,44,4).NE.0) RETURN
NAMPRO(LLL:)='TG'//VERSN
IF(DELF(NAMPRO,IDEV,20,4).NE.0) RETURN
DELDB = 0
END
SUBROUTINE DBFIX(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+GEL,GEL2,IDBSIZ,KBIN,KBOUT,IDEVR,IDEVW,IDEVN,
+IHELPS,IHELPE,IHELP1,IHELP2,FILEH,IDEVH,MAXGEL,MAXGLM,
+IDEVT,IDEVC,TEMP)
CHARACTER FILEH*(*)
C AUTHOR: RODGER STADEN
C 12-12-90 Added function to change raw data parameter file
C and changed menu routines accordingly
INTEGER RELPG(IDBSIZ),X,TEMP(IDBSIZ)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL)
CHARACTER NAME*16,NEWNAM*16
INTEGER L,M,N
CHARACTER GEL2(MAXGEL)
PARAMETER (MAXPRM = 32)
CHARACTER PROMPT(9)*(MAXPRM)
INTEGER GCLIN,CHAINL
EXTERNAL GCLIN,CHAINL
WRITE(KBOUT,1000)
1000 FORMAT(
+' Warning:',
+' make a copy first, and check logical consistency after use')
10 CONTINUE
C
C SELECT OPTION
C CALL BELL(1,KBOUT)
C DBMENU now defunct for bap - so we use RADION instead
C CALL DBMENU(4,NOPT,KOPT,IHELPS,IHELPE,FILEH,IDEVH,
C +KBIN,KBOUT)
PROMPT(1) = 'Line change'
PROMPT(2) = 'Check logical consistency'
PROMPT(3) = 'Delete contig line'
PROMPT(4) = 'Shift'
PROMPT(5) = 'Move gel reading'
PROMPT(6) = 'Rename gel reading'
PROMPT(7) = 'Break a contig'
PROMPT(8) = 'Remove a gel reading'
PROMPT(9) = 'Alter raw data parameters'
NOPT = 1
CALL RADION('Alter relationships', PROMPT, 9, NOPT, IHELPS,
+ IHELPE, FILEH, IDEVH, KBIN, KBOUT)
IF(NOPT.LT.1)RETURN
IF(NOPT.EQ.1)THEN
C LINE CHANGE
MN = 0
MX = IDBSIZ
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of line to change',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.EQ.0) GO TO 18
LNO = IVAL
IF(LNO.EQ.IDBSIZ)GO TO 19
WRITE(KBOUT,*)'Current line'
WRITE(KBOUT,1001)RELPG(LNO),LNGTHG(LNO),LNBR(LNO),RNBR(LNO)
1001 FORMAT(' ',4I6)
MN = 0
MX = 99999
X = RELPG(LNO)
CALL GETINT(MN,MX,X,
+ 'Relative position',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
X = IVAL
MN = -MAXGEL
MX = 999999
L = LNGTHG(LNO)
CALL GETINT(MN,MX,L,
+ 'Length',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
L = IVAL
MN = 0
MX = IDBSIZ
M = LNBR(LNO)
CALL GETINT(MN,MX,M,
+ 'Left neighbour',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
M = IVAL
MN = 0
MX = IDBSIZ
N = RNBR(LNO)
CALL GETINT(MN,MX,N,
+ 'Right neighbour',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
N = IVAL
CALL WRITER(IDEVR,LNO,X,L,M,N)
RELPG(LNO)=X
LNGTHG(LNO)=L
LNBR(LNO)=M
RNBR(LNO)=N
GO TO 10
18 CONTINUE
C
C deal with record 1/0 which contains: maxdb,actualdbsiz,maxgel,idm
C
WRITE(KBOUT,*)
+ 'Extreme caution: after this record is changed the program'
WRITE(KBOUT,*)
+ 'should be restarted, and could malfunction!'
CALL READR(IDEVR,0,IMSIZ,IASIZ,MXG,IDA)
WRITE(KBOUT,*)'Current line'
WRITE(KBOUT,1001)IMSIZ,IASIZ,MXG,IDA
MN = 0
MX = 999999
X = IMSIZ
CALL GETINT(MN,MX,X,
+ 'Maximum database size',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
X = IVAL
MN = 0
MX = X
L = IASIZ
CALL GETINT(MN,MX,L,
+ 'Actual database size',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
L = IVAL
MN = 0
MX = MAXGLM
M = MXG
CALL GETINT(MN,MX,M,
+ 'Maximum reading length',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
M = IVAL
ID = 0
IF(IDA.EQ.26) ID = 1
CALL YESONO(ID,'Database is for DNA',
+ 'Database is for protein',
+ IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(ID.LT.0) GO TO 10
N = 5
IF(ID.EQ.0)N = 5
IF(ID.EQ.1)N = 26
CALL WRITER(IDEVR,0,X,L,M,N)
GO TO 10
19 CONTINUE
C NCONTS NGELS LINES
MN = 0
MX = IDBSIZ
LL = NGELS
CALL GETINT(MN,MX,LL,
+ 'Number of gel readings',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
LL = IVAL
MN = 0
MX = IDBSIZ
MM = NCONTS
CALL GETINT(MN,MX,MM,
+ 'Number of contigs',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
MM = IVAL
CALL WRITER(IDEVR,IDBSIZ,LL,MM,LL,MM)
NGELS=LL
NCONTS=MM
GO TO 10
END IF
C
C
IF(NOPT.EQ.4)THEN
MN = 0
MX = NGELS
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of first gel reading to shift',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
LNO = IVAL
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,LNO)
IF(I.EQ.0)THEN
WRITE(KBOUT,*)
+ 'Problem with this gel reading. Check logical consistency'
WRITE(KBOUT,*)'of database. Shift not done'
GO TO 10
END IF
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,I)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'No contig line for this contig. Check logical'
WRITE(KBOUT,*)'consistency of database. Shift not done'
GO TO 10
END IF
MN = 1 - RELPG(LNO)
MX = RELPG(NCONTO) - RELPG(LNO)
X = MN
CALL GETINT(MN,MX,X,
+ 'Distance to shift',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
X = IVAL
CALL SHIFTC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDEVR,
+ IDBSIZ,LNO,NCONTO,X)
WRITE(KBOUT,*)'Shift complete'
GO TO 10
END IF
C
IF (NOPT.EQ.2) THEN
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ TEMP,IERR,KBOUT)
GO TO 10
END IF
IF(NOPT.EQ.3)THEN
WRITE(KBOUT,*)'Remove a contig'
MN = 0
MX = NGELS
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of a reading in the contig to delete',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.EQ.0) GO TO 10
LNO = IVAL
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,LNO)
ICONT = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,I)
IF(ICONT.EQ.0) THEN
WRITE(KBOUT,*)'No contig line for this reading'
GO TO 10
END IF
CALL REMCON(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ ICONT,GEL,I,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT,TEMP)
END IF
IF(NOPT.EQ.6)THEN
MN = 0
MX = NGELS
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of gel reading to rename',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
LNO = IVAL
CALL READN(IDEVN,LNO,NAME)
L = 16
CALL GTSTR('name for gel reading',
+ NAME,NEWNAM,L,KBOUT,KBIN,INFLAG)
IF(L.GT.0)CALL WRITEN(IDEVN,LNO,NEWNAM)
GO TO 10
END IF
IF(NOPT.EQ.5)THEN
MN = 0
MX = NGELS
IFROM = 0
CALL GETINT(MN,MX,IFROM,
+ 'Number of gel reading to move',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
IFROM = IVAL
MN = 0
MX = NGELS
ITO = 0
CALL GETINT(MN,MX,ITO,
+ 'New number for gel reading',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
ITO = IVAL
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ GEL,IFROM,ITO,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
GO TO 10
END IF
IF(NOPT.EQ.7)THEN
CALL BREAKC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,KBIN,KBOUT,IDEVR,IDEVW,IDEVN,
+ IHELPS,IHELPE,IHELP1,IHELP2,FILEH,IDEVH,IOK)
GO TO 10
END IF
IF(NOPT.EQ.8) THEN
CALL REMGD(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ KBIN,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
GO TO 10
END IF
IF(NOPT.EQ.9) THEN
CALL FIXRD(IDEVT,IDEVC,IDBSIZ,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH)
GO TO 10
END IF
GO TO 10
END
SUBROUTINE REMCON(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ICONT,GEL,LLINO,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT,TEMP)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),TEMP(IDBSIZ)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL)
C
C problem is to remove a contig. Strategy is to find all its read numbers
C and store them in temp. Then go thru and replace them by reads from the
C end of the list of reads. An earlier version tried to chain thru but
C ran into complications about replacing reads by reads they pointed to!
C
DO 10 I=1,IDBSIZ
TEMP(I) = 0
10 CONTINUE
C
NDEL = 0
I = LLINO
20 CONTINUE
TEMP(I) = 1
NDEL = NDEL + 1
IF (RNBR(I).NE.0) THEN
I = RNBR(I)
GO TO 20
END IF
C
C now in temp all the reads in the contig are 1, the rest of temp is zero
C let i be the read to move and j the last read left in the list of reads
C so if temp(i) is 1 and temp(j) is zero move read j to i and set j = j - 1
C then deal with the next i.
C if temp(i) is 1 and temp(j) is also 1 simply set j = j - 1 and try to move
C that one
C we stop when weve gone so far along the list that the next read to
C delete is equal to the number of reads left in the list
C
C what are the difficult cases?
C 1. only one contig
C 2. all reads to right of llino are are near the end of the list of reads
C
I = 1
J = NGELS
30 CONTINUE
IF (TEMP(I).EQ.1) THEN
IF (TEMP(J).EQ.0) THEN
WRITE(*,*)'MOVE ',J,' TO ',I
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,J,NCONTS,IDBSIZ,
+ GEL,J,I,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
J = J - 1
ELSE
J = J - 1
IF (I.LT.J) GO TO 30
END IF
END IF
IF (I.LT.J) THEN
I = I + 1
GO TO 30
END IF
C
C fix up number of reads and the contig record
C
NGELS = NGELS - NDEL
CALL REMCNL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ICONT,IDEVR)
END
SUBROUTINE REMGD(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+KBIN,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER HELPF*(*),GEL(MAXGEL)
INTEGER REMME,GCLIN,CHAINL
EXTERNAL GCLIN,CHAINL
C assumes db is logical consistent
WRITE(KBOUT,*)'Remove reading from database'
REMME = NGELS
CALL GETINT(1,NGELS,REMME,
+'Number of reading to remove',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
REMME = IVAL
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,REMME)
ICONT = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,I)
IF(ICONT.EQ.0) THEN
WRITE(KBOUT,*)'No contig line for this reading'
IOK = 1
RETURN
END IF
CALL REMGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+REMME,ICONT,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN)
END
SUBROUTINE REMGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+REMME,ICONT,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN)
C Routine to remove a reading from a database
C Cases: 1 left end
C 2 right end
C 3 internal and dispensible
C 4 internal and indispensible
C if 1 change contig lnbr, contig length, lnbr of rnbr of remme, relpgs
C if 2 change contig rnbr, contig length, rnbr of lnbr of remme
C if 3 change contig length, lnbr of rnbr of remme rnbr of lnbr of remme
C if 4 need to break contig, then as for 1
C if 1 and 2 then also remove contig line
C for all cases move gel ngels to remme (if remme/=ngels)
C and update line idbsiz
C
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER REMME,CLEN
LOGICAL LEFTE,RIGHTE,DISPEN
CHARACTER GEL(MAXGEL)
EXTERNAL CLEN
LEFTE = .FALSE.
RIGHTE = .FALSE.
DISPEN = .FALSE.
C
C Left end ?
C
IF(LNBR(REMME).EQ.0) LEFTE = .TRUE.
C
C Right end ?
C
IF(RNBR(REMME).EQ.0) RIGHTE = .TRUE.
C
C If both true remove the contig line, then overwrite the gel
C
IF(LEFTE.AND.RIGHTE) THEN
WRITE(KBOUT,*)'Removing reading and contig'
IFROM = NGELS
NGELS = NGELS - 1
CALL REMCNL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ ICONT,IDEVR)
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
END IF
ELSE IF(LEFTE) THEN
WRITE(KBOUT,*)'Removing reading from left end of contig'
LNBR(ICONT) = RNBR(REMME)
I = 1 - RELPG(RNBR(REMME))
WRITE(KBOUT,*)'Shifting readings in contig by distance=',I
CALL SHIFTC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDEVR,
+ IDBSIZ,RNBR(REMME),ICONT,I)
I = LNBR(ICONT)
LNBR(I) = 0
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
ELSE IF(RIGHTE) THEN
WRITE(KBOUT,*)'Removing reading from right end of contig'
RNBR(ICONT) = LNBR(REMME)
I = RNBR(ICONT)
RNBR(I) = 0
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
RELPG(ICONT) = CLEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,LNBR(ICONT))
CALL WRITER(IDEVR,ICONT,RELPG(ICONT),LNGTHG(ICONT),
+ LNBR(ICONT),RNBR(ICONT))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
ELSE
C Is remme indispensible ?
NSTART = RELPG(RNBR(REMME))
I = REMME
10 CONTINUE
I = LNBR(I)
IF(I.NE.0) THEN
IF((RELPG(I)+ABS(LNGTHG(I))-1).LT.NSTART) GO TO 10
DISPEN = .TRUE.
END IF
IF(DISPEN) THEN
WRITE(KBOUT,*)
+ 'Removing dispensible reading from middle of contig'
I = LNBR(REMME)
RNBR(I) = RNBR(REMME)
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
I = RNBR(REMME)
LNBR(I) = LNBR(REMME)
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,
+ MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
RELPG(ICONT) = CLEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,LNBR(ICONT))
CALL WRITER(IDEVR,ICONT,RELPG(ICONT),LNGTHG(ICONT),
+ LNBR(ICONT),RNBR(ICONT))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
ELSE
WRITE(KBOUT,*)
+ 'Removing indispensible reading from middle of contig'
WRITE(KBOUT,*)'So breaking contig first'
IR = REMME
IL = LNBR(REMME)
ILO = LNBR(ICONT)
NCONTO = ICONT
NCONTR = IDBSIZ - NCONTS - 1
CALL CBREAK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ KBOUT,IDEVR,IDEVW,IDEVN,IR,IL,ILO,NCONTO,NCONTR,IOK)
IF(IOK.NE.0) RETURN
WRITE(KBOUT,*)'Removing reading from left end of contig'
ICONT = IDBSIZ - NCONTS
LNBR(ICONT) = RNBR(REMME)
I = 1 - RELPG(RNBR(REMME))
WRITE(KBOUT,*)'Shifting readings in contig by distance=',I
CALL SHIFTC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDEVR,
+ IDBSIZ,RNBR(REMME),ICONT,I)
I = LNBR(ICONT)
LNBR(I) = 0
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,
+ MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
END IF
END IF
END
SUBROUTINE REMCNL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+REMME,IDEVR)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER REMME
C Routine to remove a contig line from a db
C Loop deals with case of remove top contig
C Move down all lines from above
DO 10 I = REMME,IDBSIZ-NCONTS+1,-1
RELPG(I) = RELPG(I-1)
LNGTHG(I) = LNGTHG(I-1)
LNBR(I) = LNBR(I-1)
RNBR(I) = RNBR(I-1)
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
10 CONTINUE
NCONTS = NCONTS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
END
SUBROUTINE MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+GEL,FROM,TO,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
C Subroutine to move a gel from line from to line to
C Extended 22-5-91
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),FROM,TO
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER NAMGEL*16,GEL(MAXGEL)
INTEGER GCLIN,CHAINL
LOGICAL LEFTE,RIGHTE
EXTERNAL GCLIN,CHAINL
LEFTE = .FALSE.
RIGHTE = .FALSE.
C
C left end ?
C
IF(LNBR(FROM).EQ.0) LEFTE = .TRUE.
C
C right end ?
C
IF(RNBR(FROM).EQ.0) RIGHTE = .TRUE.
C
C if both true remove the contig line, then overwrite the gel
C
IF(LEFTE.AND.RIGHTE) THEN
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,FROM)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'This gel has no left neighbour but does not'
WRITE(KBOUT,*)'appear in a contig line!'
ELSE
LNBR(NCONTO) = TO
RNBR(NCONTO) = TO
CALL WRITER(IDEVR,NCONTO,RELPG(NCONTO),LNGTHG(NCONTO),
+ LNBR(NCONTO),RNBR(NCONTO))
END IF
ELSE IF(LEFTE) THEN
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,FROM)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'This gel has no left neighbour but does not'
WRITE(KBOUT,*)'appear in a contig line!'
ELSE
LNBR(NCONTO) = TO
CALL WRITER(IDEVR,NCONTO,RELPG(NCONTO),LNGTHG(NCONTO),
+ LNBR(NCONTO),RNBR(NCONTO))
END IF
ELSE IF(RIGHTE) THEN
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,FROM)
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,I)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'This gel has no right neighbour and does not'
WRITE(KBOUT,*)'appear in a contig!'
ELSE
IF(RNBR(NCONTO).NE.FROM)THEN
WRITE(KBOUT,*)
+ 'This gel has no right neighbour but does not'
WRITE(KBOUT,*)'appear in a contig line!'
ELSE
RNBR(NCONTO) = TO
CALL WRITER(IDEVR,NCONTO,RELPG(NCONTO),LNGTHG(NCONTO),
+ LNBR(NCONTO),RNBR(NCONTO))
END IF
END IF
END IF
RELPG(TO)=RELPG(FROM)
LNGTHG(TO)=LNGTHG(FROM)
LNBR(TO)=LNBR(FROM)
RNBR(TO)=RNBR(FROM)
CALL READW(IDEVW,FROM,GEL,MAXGEL)
CALL WRITEW(IDEVW,TO,GEL,MAXGEL)
CALL READN(IDEVN,FROM,NAMGEL)
CALL WRITEN(IDEVN,TO,NAMGEL)
CALL WRITER(IDEVR,TO,RELPG(TO),LNGTHG(TO),
+LNBR(TO),RNBR(TO))
C Do neighbours
IF(LNBR(FROM).NE.0) THEN
I=LNBR(FROM)
RNBR(I)=TO
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
END IF
IF(RNBR(FROM).NE.0) THEN
I=RNBR(FROM)
LNBR(I)=TO
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
END IF
CALL MOVTAG(FROM,TO)
END
SUBROUTINE DBOPEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,NAMPRO,GEL,
+IDBSIS,IDBSIZ,IERR,KBIN,KBOUT,
+IDEVR,IDEVW,IDEVN,IDEVT,IDEVC,
+MAXGEL,MAXGLM,LLINO,
+IDM,IHELPS,IHELPE,HELPF,IDEVH)
C AUTHOR: RODGER STADEN
CHARACTER GEL(MAXGLM)
INTEGER RELPG(IDBSIS)
INTEGER LNGTHG(IDBSIS),LNBR(IDBSIS),RNBR(IDBSIS)
CHARACTER NAMPRO*(*),COPYNO*4,HELPF*(*)
INTEGER IWORD,ACTF
EXTERNAL ACTF
PARAMETER (IWORD=4)
C NOTE THIS IS THE MACHINES WORD LENGTH IE HOW MANY CHARS PER WORD
CALL FILLI(RELPG,IDBSIS,0)
CALL FILLI(LNGTHG,IDBSIS,0)
CALL FILLI(LNBR,IDBSIS,0)
CALL FILLI(RNBR,IDBSIS,0)
NAMPRO(1:)=' '
IERR=1
1 CONTINUE
L = 0
CALL GTSTR('Project name',' ',NAMPRO,L,KBOUT,KBIN,INFLAG)
IF(L.LT.1) RETURN
LL = L
CALL CCASE(NAMPRO,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
GO TO 1
END IF
L = 1
CALL GTSTR('Version','0',COPYNO,L,KBOUT,KBIN,INFLAG)
CALL CCASE(COPYNO,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
GO TO 1
END IF
IF(L.LT.1) COPYNO(1:1) = '0'
C
C check if file is open
C
NAMPRO(LL+1:LL+2) = '.'//COPYNO(1:1)
IOK = ACTF(1,NAMPRO,LL,COPYNO,KBOUT)
IF (IOK.NE.0) RETURN
NAMPRO(LL+1:LL+3)='.AR'
NAMPRO(LL+4:LL+4)=COPYNO(1:1)
CALL OPENRS(IDEVN,NAMPRO,IOK,4,4)
IF(IOK.NE.0)GO TO 100
NAMPRO(LL+2:LL+3)='RL'
CALL OPENRS(IDEVR,NAMPRO,IOK,4,4)
IF(IOK.NE.0)GO TO 100
CALL READR(IDEVR,0,IDBST,IDBSIZ,MAXGEL,IDM)
C
C Do I really need to look at this value? I could simply compare
C IDBSIS with IDBSIZ which is what really counts. Cannot remember
C why IDBST is stored!!!!!!!
C
IF(IDBST.GT.IDBSIS) THEN
CALL ERROM(KBOUT,
+ 'Fatal error: database size too large for program')
GO TO 100
END IF
NAMPRO(LL+2:LL+3)='SQ'
C DEFINE RECORD LENGTH IN TERMS OF NUMBER OF CHARS PER WORD (4 ON VAX)
C AND MAXGEL SIZE
IREC=MAXGEL/IWORD
IF(MOD(MAXGEL,IWORD).NE.0)IREC=IREC+1
CALL OPENRS(IDEVW,NAMPRO,IOK,IREC,4)
IF(IOK.NE.0)GO TO 100
NAMPRO(LL+2:LL+3) = 'TG'
CALL OPENRS(IDEVT,NAMPRO,IOK,5,4)
IF(IOK.NE.0) IDEVT = -1
NAMPRO(LL+2:LL+3) = 'CC'
C COMMENT_LENGTH: 11 = (40 + long)/long
CALL OPENRS(IDEVC,NAMPRO,IOK,11,4)
IF(IOK.NE.0) IDEVC = -1
C READ A LINE FOR LUCK
CALL READW(IDEVW,1,GEL,MAXGEL)
CALL READR(IDEVR,IDBSIZ,NGELS,NCONTS,IDUM1,IDUM2)
WRITE(KBOUT,10011)NGELS,NCONTS,IDBSIZ,MAXGEL
10011 FORMAT(' Number of gel readings ',I6,' Number of contigs ',I6,/,
+' Database size ',I6,' Maximum gel reading length=',I4)
LLINO = 0
IF(NGELS.LT.1)GO TO 5
DO 3 I=1,NGELS
CALL READR(IDEVR,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
3 CONTINUE
N=IDBSIZ-NCONTS
MXT = 0
DO 4 I=N,IDBSIZ-1
CALL READR(IDEVR,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
IF(RELPG(I).GT.MXT) THEN
MXT = RELPG(I)
LLINO = LNBR(I)
END IF
4 CONTINUE
5 CONTINUE
NAMPRO(LL+2:LL+2) = COPYNO(1:1)
IERR=0
RETURN
100 CONTINUE
IOK = ACTF(2,NAMPRO,LL,COPYNO,KBOUT)
WRITE(KBOUT,9999)
9999 FORMAT(' Error encountered opening database files')
NAMPRO(LL+2:LL+2) = COPYNO(1:1)
END
SUBROUTINE DBSTAR(NAMPRO,GEL,IDBSIS,IDBSIZ,KBIN,KBOUT,
+IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,
+IERR,IHELPS,IHELPE,IDEVH,FILEH,
+MAXGEL,MAXGLM,IDM)
CHARACTER GEL(MAXGLM),FILEH*(*)
CHARACTER NAMPRO*(*)
INTEGER IWORD,ACTF
PARAMETER (IWORD=4)
EXTERNAL ACTF
IERR=1
3 CONTINUE
NAMPRO = ' '
MN = 0
CALL GTSTR('New project name',' ',NAMPRO,MN,KBOUT,KBIN,INFLAG)
IF(MN.LT.1) RETURN
LL = MIN(12,MN)
CALL CCASE(NAMPRO,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 3
END IF
NAMPRO(LL+1:LL+2) = '.0'
IOK = ACTF(1,NAMPRO,LL,'0',KBOUT)
IF (IOK.NE.0) RETURN
MN = 10
MX = IDBSIS
IDBSIZ = 50
CALL GETINT(MN,MX,IDBSIZ,
+'Database size',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 40
IDBSIZ = IVAL
5 CONTINUE
MN = 512
MX = MAXGLM
MAXIN1 = MIN(512,MAXGEL)
MAXIN = 1024
CALL GETINT(MN,MX,MAXIN,
+'Maximum gel reading length',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 40
MAXGEL = IVAL
IF(MOD(IVAL,MAXIN1).NE.0) THEN
MAXGEL = 512 + (IVAL/512)*512
WRITE(KBOUT,*)'Maximum set to',MAXGEL
END IF
CALL YESNO(IDM,'Database is for DNA',
+IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(IDM.LT.0) GO TO 40
IF(IDM.EQ.0)IDM = 5
IF(IDM.EQ.1)IDM = 26
NAMPRO(LL+1:LL+4)='.RL0'
CALL OPENRS(IDEV1,NAMPRO,IOK,4,3)
IF(IOK.NE.0)GO TO 100
WRITE(KBOUT,1004)
1004 FORMAT(' Writing new database files')
J = 0
K = 0
N = 0
M = 0
C
C Put maximum possible database size, actual size, max read length and type
C in record 0 of relationships (actually record 1, as writer adds 1).
C
CALL WRITER(IDEV1,0,IDBSIS,IDBSIZ,MAXGEL,IDM)
C
C Put zeroes in al other records
C
DO 10 I=1,IDBSIZ
CALL WRITER(IDEV1,I,J,K,M,N)
10 CONTINUE
NAMPRO(LL+2:LL+3)='SQ'
IREC=MAXGEL/IWORD
IF(MOD(MAXGEL,IWORD).NE.0)IREC=IREC+1
CALL OPENRS(IDEV2,NAMPRO,IOK,IREC,3)
IF(IOK.NE.0)GO TO 100
CALL FILLC(GEL,MAXGEL,' ')
C CALL WRITEW(IDEV2,IDBSIZ,GEL,MAXGEL)
C
C write only the first record into the working versions
C and assume others will be added when required
C
CALL WRITEW(IDEV2,1,GEL,MAXGEL)
NAMPRO(LL+2:LL+3)='AR'
CALL OPENRS(IDEV3,NAMPRO,IOK,4,3)
IF(IOK.NE.0)GO TO 100
C
C write only the first record into the names
C and assume others will be added when required
C
CALL WRITEN(IDEV3,1,' ')
C CREATE TAG FILES (TAGS AND COMMENTS)
NAMPRO(LL+2:LL+3)='TG'
CALL OPENRS(IDEVT,NAMPRO,IOK,5,3)
IF(IOK.NE.0)GO TO 100
CALL WRITTG(IDEVT,IDBSIZ,IDBSIZ,0,0,0,0)
NAMPRO(LL+2:LL+3)='CC'
C COMMENT_LENGTH: 11 = (40 + long)/long
CALL OPENRS(IDEVC,NAMPRO,IOK,11,3)
IF(IOK.NE.0)GO TO 100
CALL WRITCC(IDEVC,1,1,0,' ')
WRITE(KBOUT,1003)NAMPRO(1:LL),IDBSIZ
1003 FORMAT(' Database ',A,' version 0, size ',I6,
+' successfully started')
IERR=0
NAMPRO(LL+2:LL+2) = '0'
RETURN
40 CONTINUE
NAMPRO(LL+1:LL+2) = '.0'
IOK = ACTF(2,NAMPRO,LL,'0',KBOUT)
RETURN
100 CONTINUE
CALL ERROM(KBOUT,'Error writing database files')
NAMPRO(LL+1:LL+2) = '.0'
IOK = ACTF(2,NAMPRO,LL,'0',KBOUT)
END
SUBROUTINE FIXRD(IDEVT,IDEVC,IDBSIZ,KBIN,KBOUT,
+IHELPS,IHELPE,FILEH,IDEVH)
C FILE_NAME_LENGTH
CHARACTER NAMFIL*18,NEWNAM*18,MTYPE*4,NEWMT*4,FILEH*(*)
IF(IDEVRD.LT.0) THEN
WRITE(KBOUT,*)'No raw data file!'
RETURN
END IF
10 CONTINUE
C Change raw data record
MN = 0
MX = IDBSIZ-1
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of line to change',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
IF(IVAL.EQ.0) RETURN
LNO = IVAL
CALL READRD(IDEVT,IDEVC,LNO,LENR,LCUT,LENW,MTYPE,NAMFIL)
WRITE(KBOUT,*)'Current line'
WRITE(KBOUT,1001)LENR,LCUT,LENW,MTYPE,NAMFIL
1001 FORMAT(' ',3I6,' ',A,' ',A)
MN = 1
MX = 9999
LX = LENR
CALL GETINT(MN,MX,LX,
+ 'Length raw sequence',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
LX = IVAL
MN = 1
MX = LX
L = LCUT
CALL GETINT(MN,MX,L,
+ 'Left cutoff',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
L = IVAL
MN = 1
MX = LX
M = LENW
CALL GETINT(MN,MX,M,
+ 'Length of original working sequence',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
M = IVAL
20 CONTINUE
LNAM = 4
CALL GTSTR('Machine type',
+ MTYPE,NEWMT,LNAM,KBOUT,KBIN,INFLAG)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 20
END IF
IF(INFLAG.EQ.3) NEWMT = MTYPE
30 CONTINUE
C FILE_NAME_LENGTH
LNAM = 18
CALL GTSTR('Name for raw data file',
+ NAMFIL,NEWNAM,LNAM,KBOUT,KBIN,INFLAG)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 30
END IF
IF(INFLAG.EQ.3) NEWNAM = NAMFIL
WRITE(KBOUT,1001)LX,L,M,NEWMT,NEWNAM
CALL WRITRD(IDEVT,IDEVC,LNO,LX,L,M,NEWMT,NEWNAM)
WRITE(KBOUT,*)'New record written to disk'
GO TO 10
END
SUBROUTINE READRD(IDEVT,IDEVC,NGEL,LENR,LCUT,LENW,MTYPE,NAMFIL)
CHARACTER MTYPE*(*),NAMFIL*(*)
C COMMENT_LENGTH
CHARACTER NOTE*40
IF(IDEVT.GT.0)THEN
CALL READTG(IDEVT,NGEL,LPOS,LLEN,LCOM,LTYPE,NEXT)
CALL READCC(IDEVC,LCOM,ICNT,NEXT,NOTE)
READ(NOTE,1001,ERR=100)LENR,LCUT,LENW,MTYPE,NAMFIL
1001 FORMAT(3I6,A,A)
ENDIF
RETURN
100 CONTINUE
LENR = 0
LCUT = 0
LENW = 0
MTYPE = ' '
NAMFIL = ' '
END
SUBROUTINE WRITRD(IDEVT,IDEVC,NGEL,LENR,LCUT,LENW,MTYPE,NAMFIL)
CHARACTER MTYPE*(*),NAMFIL*(*)
INTEGER FREECC
C COMMENT_LENGTH
CHARACTER NOTE*40
IF(IDEVT.GT.0)THEN
CALL READTG(IDEVT,NGEL,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF(LCOM.EQ.0)THEN
LCOM = FREECC(IDEVC)
ENDIF
WRITE(NOTE,1001,ERR=100)LENR,LCUT,LENW,MTYPE,NAMFIL
1001 FORMAT(3I6,A,A)
NEXT = 0
CALL WRITCC(IDEVC,LCOM,ICNT,NEXT,NOTE)
ENDIF
RETURN
100 CONTINUE
END
SUBROUTINE READTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
INTEGER SWAPBO
EXTERNAL SWAPBO
IF(IDEVT.GT.0) THEN
READ(IDEVT,REC=I)LPOS,LLEN,LCOM,LTYPE,NEXT
LPOS = SWAPBO(LPOS)
LLEN = SWAPBO(LLEN)
LCOM = SWAPBO(LCOM)
NEXT = SWAPBO(NEXT)
ENDIF
END
SUBROUTINE WRITTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
INTEGER SWAPBO
EXTERNAL SWAPBO
IF (IDEVT.GT.0) THEN
WRITE(IDEVT,REC=I)SWAPBO(LPOS),SWAPBO(LLEN),
+SWAPBO(LCOM),LTYPE,SWAPBO(NEXT)
ENDIF
END
SUBROUTINE READCC(IDEVC,I,ICNT,NEXT,NOTE)
C COMMENT_LENGTH
CHARACTER NOTE*40
C COMMENT_LENGTH - 4
CHARACTER DUMM*36
INTEGER SWAPBO
EXTERNAL SWAPBO
IF(IDEVC.GT.0)THEN
READ(IDEVC,REC=1)NEXT,ICNT,DUMM
NEXT = SWAPBO(NEXT)
ICNT = SWAPBO(ICNT)
IF(I.EQ.0.OR.I.GT.ICNT)THEN
NEXT = 0
NOTE = ' '
ELSE
READ(IDEVC,REC=I)NEXT,NOTE
NEXT = SWAPBO(NEXT)
ENDIF
ENDIF
END
SUBROUTINE WRITCC(IDEVC,I,ICNT,NEXT,NOTE)
C COMMENT_LENGTH
CHARACTER NOTE*40
C COMMENT_LENGTH - 4
CHARACTER DUMM*36
INTEGER SWAPBO
EXTERNAL SWAPBO
IF(IDEVC.GT.0)THEN
IF(I.EQ.1) THEN
WRITE(IDEVC,REC=1)SWAPBO(NEXT),SWAPBO(ICNT),DUMM
ELSE
READ(IDEVC,REC=1)IDUM,ICNT,DUMM
ICNT = SWAPBO(ICNT)
IF(I.LE.ICNT) THEN
WRITE(IDEVC,REC=I)SWAPBO(NEXT),NOTE
ENDIF
ENDIF
ENDIF
END
SUBROUTINE PADCON(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+GEL,LINCON,POSN,NC,IDBSIZ,IDEVR,IDEVW,MAXGEL,KBOUT)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),POSN,X
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL)
CHARACTER PAD
SAVE PAD
DATA PAD/'*'/
C NOW FIND FIRST CHAR THAT OVERLAPS REGION
LLINO=LNBR(LINCON)
30 CONTINUE
X=RELPG(LLINO)+ABS(LNGTHG(LLINO))-1
IF(X.GE.POSN)GO TO 40
C NOT IN REGION
LLINO=RNBR(LLINO)
GO TO 30
40 CONTINUE
C NOW GET THIS GEL FROM DISK
CALL READW(IDEVW,LLINO,GEL,MAXGEL)
C CALC POSN IN THIS GEL TO EDIT
X=POSN-RELPG(LLINO)+1
K=X
C MOVE THE DATA RIGHT
M=ABS(LNGTHG(LLINO))
LNGTHG(LLINO)=LNGTHG(LLINO)+SIGN(NC,LNGTHG(LLINO))
C CHECK FOR OVER END OF ARRAY
N=ABS(LNGTHG(LLINO))
IF(N.GT.MAXGEL)THEN
WRITE(KBOUT,1000)LLINO
1000 FORMAT(
+' Data pushed off end of gel',I4,' during padding')
M=M-(N-MAXGEL)
N=MAXGEL
LNGTHG(LLINO)=SIGN(MAXGEL,LNGTHG(LLINO))
END IF
J=M-K+1
DO 55 I=1,J
GEL(N)=GEL(M)
N=N-1
M=M-1
55 CONTINUE
C PERFORM THE INSERTION
DO 60 I=K,MIN(MAXGEL,K+NC-1)
GEL(I)=PAD
60 CONTINUE
C WRITE BACK TO DISK
CALL WRITEW(IDEVW,LLINO,GEL,MAXGEL)
C WRITE NEW LINE
CALL WRITER(IDEVR,LLINO,RELPG(LLINO),LNGTHG(LLINO),
+LNBR(LLINO),RNBR(LLINO))
C NOW UPDATE TAG FILES ACCORDINGLY
CALL PADTAG(LLINO,K,NC,LNGTHG(LLINO))
65 CONTINUE
C NOW GET NEXT GEL
LLINO=RNBR(LLINO)
C LAST GEL?
IF(LLINO.EQ.0)GO TO 70
C DOES IT HAVE DATA IN REGION?
C IE DO RELPG AND RELPG+LNGTHG-1 LIE EITHER SIDE OF POSN?
IF(RELPG(LLINO).GT.POSN)GO TO 70
X=RELPG(LLINO)+ABS(LNGTHG(LLINO))-1
IF(X.LT.POSN)GO TO 65
C WITHIN
GO TO 40
70 CONTINUE
C INSERTS FINISHED SO NEED TO INCREMENT ALL THOSE GELS TO RIGHT
LLINO=LNBR(LINCON)
75 CONTINUE
IF(RELPG(LLINO).GT.POSN)GO TO 80
76 CONTINUE
LLINO=RNBR(LLINO)
IF(LLINO.EQ.0)GO TO 90
GO TO 75
80 CONTINUE
RELPG(LLINO)=RELPG(LLINO)+NC
C WRITE NEW LINE
CALL WRITER(IDEVR,LLINO,RELPG(LLINO),LNGTHG(LLINO),
+LNBR(LLINO),RNBR(LLINO))
GO TO 76
90 CONTINUE
C NEED TO INCREMENT CONTIG LINE
RELPG(LINCON)=RELPG(LINCON)+NC
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
END
SUBROUTINE AUTOJ(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
+NGELS,NCONTS,MAXGEL,
+TEMP3,WORDP,WORDN,LPOWRC,POSNS,GELN,
+SEQ1,MAXSEQ,SEQ2,SEQ3,SEQ4,SEQ5,SEQC2,SEQG2,MATCH,
+MAXGLM,MAXGL2,CHRSIZ,ECHRSZ,LENGTH,
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,CONST,
+KBIN,KBOUT,IDEV1,IDEV2,IDEV3,IDEV4,IDEV7,IDEV8,IDEV,
+IHELPS,IHELPE,HELPF,IDEVH,NAMARC,NAMPRO,FILE,
+PERCD,IOPEN,IDM,SEQG3,SEQC3,IOK,IDEVC,IDEVT)
INTEGER CHRSIZ,ECHRSZ
INTEGER RELPG(MAXDB)
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
INTEGER JOINT(2),ITOTPC(2),ITOTPG(2),IDIM22(2),IDOUT(2)
INTEGER LLINO(2),ITYPE(2),IFAIL
INTEGER ILEFTS(2),ILC(2),IPOSC(2),IPOSG(2),ISENSE(2)
INTEGER WINDOW
INTEGER TEMP3(ECHRSZ,MAXGL2),CONST(LENGTH)
INTEGER POSNS(MAXSEQ),WORDP(LPOWRC),WORDN(LPOWRC),GELN(MAXGLM)
INTEGER CENDS(MAXCON),NENDS(MAXCON)
CHARACTER SEQ3(MAXGLM),SEQC2(MAXGLM,2),SEQG2(MAXGLM,2)
CHARACTER SEQ1(MAXSEQ),SEQ2(MAXGLM),MATCH(MAXGLM),SEQ4(MAXGLM)
INTEGER SAV1(MAXSAV),SAV2(MAXSAV),SAV3(MAXSAV)
CHARACTER NAMARC*(*),NAMPRO*(*),FILE*(*)
CHARACTER SEQ5(MAXGLM),HELPF*(*),SEQG3(MAXGLM),SEQC3(MAXGLM)
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ TEMP3,IERR,KBOUT)
IF(IERR.GT.1) RETURN
IFAIL = 0
IF(NGELS.LT.1) RETURN
MN = LENGTH*2
MX = MAXGLM + 1
MINMAT = MAX(15,MN)
CALL GETINT(MN,MX,MINMAT,
+'Minimum initial match',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MINMAT = IVAL
MINSLI = 3
MN = 0
MX = 50
MAXPG = 8
CALL GETINT(MN,MX,MAXPG,
+'Maximum pads per sequence',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXPG = IVAL
MAXPC = IVAL
RMN = 0.
RMX = 100.
PERMAX = 75.
CALL GETRL(RMN,RMX,PERMAX,
+ 'Maximum percent mismatch after alignment',
+ VAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
PERMAX = VAL
MN = MINMAT
MX = MAXGEL
WINDOW = 100
CALL GETINT(MN,MX,WINDOW,
+'Probe length',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
WINDOW = IVAL
IOK = 1
I = 0
CALL YESNO(I,'Use clipped data',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(I.LT.0) RETURN
IWING = 0
IF(I.EQ.0) THEN
MN = 1
MX = MAXGEL
IWING = 100
CALL GETINT(MN,MX,IWING,
+ 'Window size for good data scan',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
IWING = IVAL
MN = 1
MX = MIN(100,IWING)
NBAD = MIN(IWING,5)
CALL GETINT(MN,MX,NBAD,
+ 'Maximum number of dashes in scan window',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
NBAD = IVAL
END IF
MAXOVR=MAXGEL-3*MAX(MAXPC,MAXPG)
IDIM2=MAXGEL
C
C Note I am doing something horrible here to save space:
C temp3 is used for cends, nends and as temp3. I can do this
C because i call fndcon to reinstate cends ,nends after each
C use of temp3 for the consensus calc. However iladd and iradd
C need the same amount of storage as cends and nends so i use
C the arrays cends and nends for them. iladd and iradd are not
C updated after use of temp3. The switch in array use is made
C by the following subroutine call
C
C replaced following line 25-9-92
C +SAV1,SAV2,SAV3,MAXSAV,TEMP3,TEMP3(MAXCON+1,1),MAXCON,
C
CALL AUTOJN(SEQ1,MAXSEQ,SEQ2,IDIM2,ILEFTS,ILC,IPOSC,
+IPOSG,ISENSE,LLINO,IMATC,IFCOMP,MINMAT,POSNS,WORDP,WORDN,
+CONST,LENGTH,LPOWRC,IDEV,MATCH,MAXGEL,MAXGLM,SEQ5,GELN,
+SAV1,SAV2,SAV3,MAXSAV,TEMP3,TEMP3(1,1+MAXCON/2),MAXCON,
+SEQG2,SEQC2,SEQ4,IDOUT,IDIM22,ITOTPG,ITOTPC,JOINT,IFAIL,
+ITYPE,MAXPC,MAXPG,PERMAX,MINSLI,SEQG3,SEQC3,KFAIL,
+WINDOW,CENDS,NENDS,RELPG,LNBR,IDBSIZ,NGELS,NCONTS,
+LNGTHG,RNBR,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,PERCD,IWING,NBAD,
+ECHRSZ,SEQ5,TEMP3,MAXGL2,IDM,NAMPRO,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH)
END
C
SUBROUTINE AUTOJN(SEQ1,MAXSEQ,GEL,IDIMGI,ILEFTS,
+ILC,IPOSC,
+IPOSG,ISENSE,LLINO,IMATC,IFCOMP,MINMAT,POSNS,WORDP,WORDN,
+CONST,LENGTH,LPOWRC,IDEV,MATCH,MAXGEL,MAXGLM,GELCOP,GELN,
+SAVPS,SAVPG,SAVL,MAXSAV,CENDS,NENDS,MAXCON,
+SEQG2,SEQC2,SEQ4,IDOUT,IDIM22,ITOTPG,ITOTPC,JOINT,IFAIL,
+ITYPE,MAXPC,MAXPG,PERMAX,MINSLI,SEQG3,SEQC3,KFAIL,
+WINDOW,ILADD,IRADD,RELPG,LNBR,IDBSIZ,NGELS,NCONTS,
+LNGTHG,RNBR,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,PERCD,IWING,NBAD,
+ECHRSZ,SEQ5,TEMP3,MAXGL2,IDM,NAMPRO,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH)
C AUTHOR: RODGER STADEN
INTEGER ECHRSZ
INTEGER ILEFTS(2),ILC(2),IPOSC(2),IPOSG(2),ISENSE(2),LLINO(2)
INTEGER POSNS(MAXSEQ),GELN(MAXGLM),WORDP(LPOWRC),SAVPS(MAXSAV)
INTEGER SAVPG(MAXSAV),SAVL(MAXSAV)
INTEGER WORDN(LPOWRC)
CHARACTER GELCOP(MAXGLM),MATCH(MAXGLM),NAMPRO*(*),HELPF*(*)
INTEGER CENDS(MAXCON),NENDS(MAXCON),ILADD(MAXCON),IRADD(MAXCON)
INTEGER CONST(LENGTH)
CHARACTER SEQ1(MAXSEQ),GEL(MAXGLM),SEQ5(MAXGLM)
CHARACTER SEQG2(MAXGLM,2),SEQC2(MAXGLM,2),SEQ4(MAXGLM)
INTEGER IDOUT(2),IDIM22(2),ITOTPG(2),ITOTPC(2),JOINT(2)
INTEGER IFAIL,ITYPE(2)
PARAMETER (MAXC = 100)
CHARACTER SEQG3(MAXGLM),SEQC3(MAXGLM)
INTEGER JLEFTS(MAXC),JLC(MAXC),JPOSC(MAXC),JPOSG(MAXC),MCON(MAXC)
INTEGER JSENSE(MAXC),JLLINO(MAXC),WINDOW,CSTART
INTEGER RELPG(IDBSIZ),LNBR(IDBSIZ),LNGTHG(IDBSIZ),RNBR(IDBSIZ)
INTEGER TEMP3(ECHRSZ,MAXGL2)
INTEGER CLINNO,CHAINL,XVERSN
EXTERNAL CLINNO,CHAINL,XVERSN
IEXT = 0
IF (IWING.NE.0) IEXT = 1
IFAIL = 1
KFAIL = 0
C
C calc the consensus and add the unused data if required
C save the lengths of the unused data in iladd, iradd
C
CALL FILLI(ILADD,NCONTS,0)
CALL FILLI(IRADD,NCONTS,0)
IDIM = 0
JOB = 0
CALL JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,GEL,IDBSIZ,IDIM,JOB,KDUMM,KDUMM,KDUMM,KDUMM,
+TEMP3,
+ECHRSZ,MAXGL2,KBOUT,IDEV2,IFAIL,MAXGEL,IDM,PERCD,SEQ5,
+ILADD,IRADD,MAXCON,KDUMM,IWING,NBAD)
IDCEND=MAXCON
CALL FNDCON(SEQ1,IDIM,CENDS,NENDS,IDCEND,MAXCON,KBOUT)
C WRITE(*,*)'IDIM',IDIM
C WRITE(*,*)(CENDS(K),NENDS(K),K=1,IDCEND)
C
C find possible missed joins
C we have consensus in seq1 in order first contig,second contig etc
C compare the ends in reverse order, simultaneously shortening the consensus
C the total consensus length is denoted by idimin
C but we compare the last contig to the rest so denote the length
C of the rest by idim
C
NFOUND = 0
NMADE = 0
C
C init hashing constants
C
CALL INITE(CONST,CSTART,LENGTH)
C
C idim is the length up to the end of the last but 1 consensus
C (we get from the start of the last contig)
C jcon is the last contig (ie the one we are currently comparing)
C
JCON = IDCEND + 1
C
C come here for the next contig
C
10 CONTINUE
C
C
IDIMIN = IDIM
C WRITE(*,*)'IDIM,IDIMIN',IDIM,IDIMIN
JCON = JCON - 1
C
C come here if weve just made a join
C
20 CONTINUE
C
C
C WRITE(*,*)'*********COMPARING CONTIG',JCON
IF (JCON.GT.1) THEN
C WRITE(*,*)'IDCEND,JCON'
C WRITE(*,*)IDCEND,JCON
C WRITE(*,1222)
C + (K,NENDS(K),CENDS(K),ILADD(K),IRADD(K),K=1,JCON)
C 1222 FORMAT(5I6)
C WRITE(*,*)(ILADD(K),IRADD(K),K=1,JCON)
IDIM = CENDS(JCON) - 1
C WRITE(*,*)'IDIM,IDIMIN',IDIM,IDIMIN
CALL ENCOF(SEQ1,IDIM,CONST,CSTART,LENGTH,POSNS)
CALL ENCONN(POSNS,IDIM,WORDP,WORDN,LPOWRC,LENGTH,1)
C
C point to probes at the ends of the current contig
C
JS = CENDS(JCON) + 20
JE = CENDS(JCON+1) - 1
IEND = 1
IDIMG = MIN(WINDOW,JE-JS+1)
C
C check for case where contig is shorter than probe (window)
C in which case only compare the left hand end
C
IF(JE-JS+1.LE.WINDOW) IEND = 2
C
C come here for left end of contig
C
30 CONTINUE
C
C
C WRITE(*,*)'JCON,JS,JE,IDIMG'
C WRITE(*,*)JCON,JS,JE,IDIMG
IMATC = 0
IF(IEND.EQ.1) THEN
CALL SQCOPY(SEQ1(JE-IDIMG+1),GEL,IDIMG)
ELSE
CALL SQCOPY(SEQ1(JS),GEL,IDIMG)
END IF
CALL SQCOPY(GEL,GELCOP,IDIMG)
ISTRAN=1
C
C come here for strand 2
C
40 CONTINUE
C
C
CALL ENCOF(GEL,IDIMG,CONST,CSTART,LENGTH,GELN)
IDSAV=MAXSAV
CALL CFGEL(GELN,IDIMG,POSNS,IDIM,WORDP,WORDN,LENGTH,LPOWRC,
+ SAVPG,SAVPS,SAVL,
+ IDSAV,SEQ1,GEL,MINMAT,IFCOMP,IDEV)
IF(IFCOMP.NE.0) THEN
CALL ERROM(KBOUT,'Error in CFGEL')
RETURN
END IF
IF(IDSAV.NE.0)THEN
CALL ADISM5(IDIM,IDIMG,SAVPS,SAVPG,IDSAV,CENDS,NENDS,
+ IDCEND,MAXCON,JLEFTS,JLC,JPOSC,JPOSG,JSENSE,JLLINO,
+ IMATC,ISTRAN,MAXC,KBOUT,MCON)
END IF
ISTRAN=ISTRAN+1
C
C have we done both strands for this probe ?
C
IF(ISTRAN.EQ.2) THEN
CALL SQCOPY(GELCOP,GEL,IDIMG)
CALL SQREV(GEL,IDIMG)
CALL SQCOM(GEL,IDIMG)
GO TO 40
END IF
CALL SQCOPY(GELCOP,GEL,IDIMG)
KSENSE = 0
C WRITE(KBOUT,*)'Total matches found',IMATC
C CALL FMTDB(SEQ1,IDIMIN,1,IDIMIN,60,KBOUT)
IF(IMATC.NE.0) THEN
JMATC = 0
C
C loop for all matches on both strands
C
DO 100 I = 1,IMATC
IF(JSENSE(I).EQ.-1) THEN
IF(KSENSE.EQ.0) THEN
CALL SQREV(GEL,IDIMG)
CALL SQCOM(GEL,IDIMG)
KSENSE = 1
END IF
END IF
JDIM22 = IDIMG
JDOUT = MAXGEL
IDSAV = MAXSAV
CALL ALINEJ(SEQ1(JLEFTS(I)),GEL,SEQG3,SEQC3,
+ SAVPS,SAVPG,SAVL,IDSAV,JLC(I),JDIM22,JDOUT,
+ JPOSC(I),JPOSG(I),MINSLI,JJOINT,JTOTPC,JTOTPG,
+ JFAIL,JTYPE,MAXPC,MAXPG,PERMAX,KBOUT,IDEV,
+ SEQ4,MAXGEL,PERMS,
+ NENDS(JCON),IEND,JLLINO(I),JSENSE(I),ILADD,IRADD,MAXCON,
+ MCON(I),
+ JCON,RELPG,LNBR,IDBSIZ,NCONTS,NFOUND,IENDCT,IENDGT)
IF (JFAIL.NE.0) GO TO 100
C
C if this is the x version and the results are being shown on the screen
C we can offer the join editor and make the join
C
IF ((XVERSN().NE.0).AND.(IDEV.EQ.KBOUT)) THEN
C
C another horrible thing here: sending posns for use by dbchek after
C a join is made (only used then)
C
CALL USJED(
+ SEQ1,MAXSEQ,IDIMIN,IDIM,GEL,KBIN,KBOUT,MAXGEL,MAXGLM,
+ CENDS,NENDS,MAXCON,IFAIL,MCON(I),JCON,NAMPRO,
+ JSENSE(I), JLLINO(I),
+ ILADD,IRADD,RELPG,LNBR,IDBSIZ,NGELS,
+ NCONTS,
+ LNGTHG,RNBR,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,
+ PERCD,IWING,NBAD,
+ IENDGT,IENDCT,SEQ4,IDCEND,IEXT,
+ ECHRSZ,SEQ5,TEMP3,MAXGL2,IDM,
+ IHELPS,IHELPE,HELPF,IDEVH,POSNS,NMADE,IOK)
IF (IFAIL.NE.0) GO TO 200
IF (NCONTS.EQ.1) GO TO 200
IF (IOK.EQ.2) GO TO 200
C
C if join has been made, assume everything is tidy and do this contig again
C
IF (IOK.EQ.0) GO TO 20
END IF
100 CONTINUE
END IF
IEND = IEND + 1
C
C have we done both ends of this contig ?
C
IF(IEND.EQ.2) GO TO 30
C
C do the next contig
C
GO TO 10
END IF
C
C jump here if only one contig left ! or user wants to escape
C
200 CONTINUE
WRITE(KBOUT,*)'Number of potential joins found',NFOUND
WRITE(KBOUT,*)'Number of joins made',NMADE
END
SUBROUTINE USJED(
+SEQ1,MAXSEQ,IDIMIN,IDIM,GEL,KBIN,KBOUT,MAXGEL,MAXGLM,
+CENDS,NENDS,MAXCON,IFAIL,MCON,JCON,NAMPRO,JSENSE,JLLINO,
+ILADD,IRADD,RELPG,LNBR,IDBSIZ,NGELS,NCONTS,
+LNGTHG,RNBR,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,PERCD,IWING,NBAD,
+IENDGT,IENDCT,SEQ2,IDCEND,IEXT,
+ECHRSZ,SEQ5,TEMP3,MAXGL2,IDM,IHELPS,IHELPE,HELPF,IDEVH,
+TEMP1,NMADE,IOK)
C AUTHOR: RODGER STADEN
INTEGER ECHRSZ
INTEGER CENDS(MAXCON),NENDS(MAXCON),ILADD(MAXCON),IRADD(MAXCON)
CHARACTER SEQ1(MAXSEQ),GEL(MAXGLM),SEQ5(MAXGLM),SEQ2(MAXGEL)
INTEGER JSENSE,JLLINO,MCON,TEMP1(IDBSIZ)
INTEGER RELPG(IDBSIZ),LNBR(IDBSIZ),LNGTHG(IDBSIZ),RNBR(IDBSIZ)
INTEGER TEMP3(ECHRSZ,MAXGL2)
INTEGER CLINNO,CHAINL
CHARACTER HELPF*(*),NAMPRO*(*)
EXTERNAL CLINNO,CHAINL
C WRITE(*,*)'CURRENT MAX CONSENSUS LENGTH',MAXSEQ
C WRITE(*,*)'CURRENT CONSENSUS LENGTH',IDIM
C WRITE(*,*)'MAXGEL,MAXGLM,MAXCON',MAXGEL,MAXGLM,MAXCON
C WRITE(*,*)'NGELS,NCONTS',NGELS,NCONTS
C
C routine to offer use of join editor and if join is made tidy up
C
IFAIL = 0
IOK = 2
IJOIN = 0
CALL YESNO(IJOIN,'Use the editor',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(IJOIN.LT.0) RETURN
IOK = 1
IF (IJOIN.EQ.0) THEN
C
C weve called the editor
C
C
C the contig names are nends(jcon) and jllino(i)
C if jsense is -1 the contig to complement is nends(jcon)
C the position of the overlap is iendct in jllino(i) and iendgt in nends(jcon)
C we are going to need to know the endpoints of the consensuses to delete
C the element number in nends of one contig is mcon(i) and the other is jcon
C cends(i) stores the position relative to the consensus of the left end
C of contig i
C
C WRITE(*,*)'NENDS(JCON)',NENDS(JCON)
C WRITE(*,*)'IDBSIZ,NCONTS',IDBSIZ,NCONTS
IF (JSENSE.EQ.-1) THEN
LINCON = CLINNO(LNBR,IDBSIZ,NCONTS,NENDS(JCON))
IF (LINCON.EQ.0) THEN
C
C major cockup here: weve lost the contig number
C
CALL ERROM(KBOUT,
+ 'Error: contig line not found for complementing')
IFAIL = 1
RETURN
END IF
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ LINCON,NENDS(JCON),GEL,IDBSIZ,KBOUT,IDEV1,IDEV2,MAXGEL)
NENDS(JCON) = LNBR(LINCON)
END IF
C
C note the number of contigs
C
NCIN = NCONTS
C WRITE(*,*)'JCON,NENDS(JCON)',JCON,NENDS(JCON)
LNCONL = CLINNO(LNBR,IDBSIZ,NCONTS,NENDS(JCON))
IF (LNCONL.EQ.0) THEN
C
C major cockup here: weve lost the contig number
C
CALL ERROM(KBOUT,
+ 'Error: contig line not found for left contig')
IFAIL = 1
RETURN
END IF
C WRITE(*,*)'I,MCON,NENDS(MCON)',I,MCON,NENDS(MCON)
LNCONR = CLINNO(LNBR,IDBSIZ,NCONTS,NENDS(MCON))
IF (LNCONR.EQ.0) THEN
C
C major cockup here: weve lost the contig number
C
CALL ERROM(KBOUT,
+ 'Error: contig line not found for right contig')
IFAIL = 1
RETURN
END IF
C WRITE(*,*)IDBSIZ,LNCONL,NENDS(JCON),LNCONR,NENDS(MCON)
C WRITE(*,*)IENDGT,IENDCT,PERCD,NGELS,NCONTS
C
C call the editor
C
CALL JXEDIT(IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,
+ RELPG,LNGTHG,LNBR,RNBR,MAXGEL,
+ IDBSIZ,LNCONR,NENDS(MCON),LNCONL,NENDS(JCON),
+ 0,IENDCT,0,IENDGT,PERCD,NGELS,NCONTS,IDM,IEXT,JOK)
C
C jok 0 = nothing done
C 1 = left contig saved
C 2 = right contig saved
C 3 = both contigs saved
C 7 = join made
C we could use these values but we dont: we only count contigs.
C if a contig is saved its consensus may be different. For now dont worry!!!!
C
C
C note we may not have joined but may have either
C complemented a contig or edited one! We shall ignore the edited
C contig, but must uncomplement the contig. See below.
C Remove the 2 consensus sequences
C Add the new one to the right end
C Update nends, cends
C Update iladd iradd, and add the new data to the end of the list
C to update iladd, iradd move all data left one element
C
IF (NCIN.GT.NCONTS) THEN
C
C weve made a join
C
NMADE = NMADE + 1
C
C check for consistency
C
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ TEMP1,IFAIL,KBOUT)
IF (IFAIL.NE.0) RETURN
C
C sometimes there may only be one contig now!
C
IF (NCONTS.EQ.1) RETURN
C
C get contig left gel number
C
LLINOC = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,NENDS(JCON))
IF (LLINOC.EQ.0) THEN
CALL ERROM(KBOUT,'Gel number not in a contig')
IFAIL = 1
RETURN
END IF
C
C get contig line number
C
LINCON = CLINNO(LNBR,IDBSIZ,NCONTS,LLINOC)
IF (LINCON.EQ.0) THEN
CALL ERROM(KBOUT,'Error: contig line not found')
IFAIL = 1
RETURN
END IF
C WRITE(*,*)'DELETE CONSENSUS FROM',CENDS(MCON)
C WRITE(*,*)'TO',CENDS(MCON+1)
C WRITE(*,*)'SHORTEN THE CONSENSUS BY'
C WRITE(*,*)CENDS(MCON+1)-CENDS(MCON)
C WRITE(*,*)CENDS(JCON+1)-CENDS(JCON)
C
C shift the consensus to delete the internal consensus then
C reduce idim,idimin accordingly (for both contigs). Finally
C move the extension sizes into the appropriate elements.
C
CALL SHFTLA(SEQ1,MAXSEQ,CENDS(MCON+1),CENDS(MCON),
+ IDIMIN)
IDIM = IDIM - (CENDS(JCON+1)-CENDS(JCON))
IDIMIN = IDIMIN - (CENDS(JCON+1)-CENDS(JCON))
IDIM = IDIM - (CENDS(MCON+1)-CENDS(MCON))
IDIMIN = IDIMIN - (CENDS(MCON+1)-CENDS(MCON))
DO 50 J=MCON,NCONTS-1
ILADD(J) = ILADD(J+1)
IRADD(J) = IRADD(J+1)
50 CONTINUE
C
C make a consensus for the joined contig, putting it at the end
C
JOB = 1
JCON = JCON - 1
CALL JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+ SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIMIN,JOB,LLINOC,LINCON,1,
+ RELPG(LINCON),TEMP3,
+ ECHRSZ,MAXGL2,KBOUT,IDEV2,IFAIL,MAXGEL,IDM,PERCD,SEQ5,
+ ILADD,IRADD,MAXCON,JCON,IWING,NBAD)
IF (IFAIL.NE.0) RETURN
C
C now restore the contig end positions because jcons has overwritten them
C (they have changed anyway)
C
CALL FNDCON(SEQ1,IDIMIN,CENDS,NENDS,IDCEND,MAXCON,KBOUT)
IOK = 0
C
C end of join made
C
ELSE
C
C if we get here we have called the editor but not made a join
C so we might need to tidy up
C
IF (JSENSE.EQ.-1) THEN
LINCON = CLINNO(LNBR,IDBSIZ,NCONTS,NENDS(JCON))
IF (LINCON.EQ.0) THEN
C
C major cockup here: weve lost the contig number
C
CALL ERROM(KBOUT,
+ 'Error: contig line not found for complementing')
IFAIL = 1
RETURN
END IF
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ LINCON,NENDS(JCON),GEL,IDBSIZ,KBOUT,IDEV1,IDEV2,
+ MAXGEL)
NENDS(JCON) = LNBR(LINCON)
END IF
END IF
END IF
END
SUBROUTINE ALINEJ(SEQ1,SEQ2,SEQG2,SEQC2,ISAV1,ISAV2,ISAV3,
+IDSAV,IDC,IDIM2,IDOUT,IC1,IG1,MINSLI,JOINT,
+ITOTPC,ITOTPG,IFAIL,ITYPE,MAXPC,MAXPG,PERMAX,KBOUT,IDEV,
+SEQ3,MAXGEL,
+PERCM,JCONN,IEND,NCON,JSENSE,ILADD,IRADD,MAXCON,MCON,JCON,
+RELPG,LNBR,IDBSIZ,NCONTS,NFOUND,IENDCT,IENDGT)
C AUTHOR: RODGER STADEN
CHARACTER SEQ1(IDC),SEQ2(IDIM2),SEQG2(IDOUT),SEQC2(IDOUT)
CHARACTER SEQ3(MAXGEL)
INTEGER ISAV1(IDSAV),ISAV2(IDSAV),ISAV3(IDSAV)
INTEGER ILADD(MAXCON),IRADD(MAXCON)
INTEGER RELPG(IDBSIZ),LNBR(IDBSIZ),WINDOW
MINSLT=MINSLI
C SAVE SEQ2
CALL SQCOPY(SEQ2,SEQ3,IDIM2)
IFAIL=1
C FIND MATCHES
IPP=IDSAV
CALL SLIDER(SEQ1,IDC,SEQ3,IDIM2,IC1,IG1,MAXPG,MAXPC,MINSLT,
+ISAV1,ISAV2,ISAV3,IPP)
IF(IPP.GT.IDSAV)RETURN
IF(IPP.LT.1)RETURN
CALL REMOVL(ISAV2,ISAV3,ISAV1,IPP)
CALL BUB3AS(ISAV2,ISAV3,ISAV1,IPP)
C DO TOPOLOGICAL CHECK
CALL TPCHEK(ISAV2,ISAV3,ISAV1,IPP)
IFAIL=0
C
C save idim2 as window
C
WINDOW = IDIM2
CALL LINEUP(SEQ2,SEQ1,SEQG2,SEQC2,IDC,IDIM2,IDOUT,ISAV3,ISAV2,
+ISAV1,IPP,ITOTPC,ITOTPG,JOINT,ITYPE,KBOUT,MAXGEL,IFAIL)
IF(IFAIL.NE.0)RETURN
C IDIM2 IS NOW LENGTH OF ALIGNED GEL
CALL JALIGN(SEQC2,SEQG2,SEQ3,MAXGEL,IDOUT,IDIM2,JOINT,
+ITYPE,PERCM,KBOUT,IDEV,IFAIL,PERMAX,JCONN,IEND,NCON,JSENSE,
+ILADD,IRADD,MAXCON,MCON,JCON,RELPG,LNBR,IDBSIZ,NCONTS,WINDOW,
+NFOUND,IENDCT,IENDGT)
IF (ITOTPC.GT.MAXPC) IFAIL = 1
IF (ITOTPG.GT.MAXPG) IFAIL = 1
IF (PERCM.GT.PERMAX) IFAIL = 1
END
C
C COUNTS MISMATCHES AND DISPLAYS OVERLAP.
SUBROUTINE JALIGN(SEQC2,SEQG2,SEQ3,MAXGEL,IDOUT,IDIM2,
+JOINT,ITYPE,X,KBOUT,IDEV,IFAIL,PERMAX,JCONN,IEND,NCON,JSENSE,
+ILADD,IRADD,MAXCON,MCON,JCON,RELPG,LNBR,IDBSIZ,NCONTS,WINDOW,
+NFOUND,IENDCT,IENDGT)
C AUTHOR: RODGER STADEN
CHARACTER SEQC2(MAXGEL),SEQG2(MAXGEL),SEQ3(MAXGEL)
CHARACTER PAD,DASH,STRAND,NAME1*6,NAME2*6
INTEGER ILADD(MAXCON),IRADD(MAXCON),RELPG(IDBSIZ),LNBR(IDBSIZ)
INTEGER CLINNO,WINDOW
EXTERNAL CLINNO
SAVE PAD,DASH
DATA PAD,DASH/',','-'/
C
C where are the overlaps?
C
C if ITYPE is 1 the overlap starts within the reading at JOINT
C else it starts at the left end of the reading at JOINT in the contig
C
C
IENDG=1
IENDC=JOINT
C ONLY LOOK AT OVERLAP WHICH IS FROM JOINT FOR LEFT TYPE JOIN
IF(ITYPE.EQ.1)THEN
IENDG=JOINT
IENDC=1
END IF
C LENGTH OF OVERLAP?
LG=IDIM2-IENDG+1
LO=MIN(IDOUT,LG)
C SAVE RAW DATA
CALL SQCOPY(SEQG2,SEQ3,IDIM2)
X=REAL(LO)
Y=X
K=IENDG+LO-1
C POINT TO CONSENSUS
J=0
C CHECK FOR OVERFLOW
IF(K.GT.MAXGEL)THEN
CALL ERROM(KBOUT,'Matching region too long in JALIGN')
IFAIL=1
RETURN
END IF
DO 200 I=IENDG,K
J=J+1
IF(SEQC2(J).EQ.SEQ3(I))GO TO 200
C IF(SEQ3(I).EQ.DASH)GO TO 200
C IF(SEQC2(J).EQ.DASH)GO TO 200
C IF(SEQC2(J).EQ.PAD)GO TO 200
X=X-1.
200 CONTINUE
X=(Y-X)*100./Y
IF(X.LT.PERMAX) THEN
IC = CLINNO(LNBR,IDBSIZ,NCONTS,JCONN)
IF(IC.EQ.0) THEN
CALL ERROM(KBOUT,'Error: contig line not found')
IFAIL = 99
RETURN
END IF
IF(JSENSE.EQ.-1) THEN
STRAND = '-'
IF(IEND.EQ.1) THEN
C
C probe is complement of right hand end of contig. Give posns assuming
C this contig is complemented.
C
IENDGT = IENDG - IRADD(JCON)
C
C Next line gives posns relative to original orientation
C IENDGT = RELPG(IC) + IRADD(JCON) - IENDG + 1
ELSE
C
C probe is complement of left end of contig. Give posns assuming this
C contig is going to be complemented.
C
IENDGT = RELPG(IC) - WINDOW + ILADD(JCON) + IENDG
END IF
ELSE
STRAND = '+'
IF(IEND.EQ.2) THEN
C
C probe is left hand end of contig in original sense
C
IENDGT = IENDG - ILADD(JCON)
ELSE
C
C probe is right hand end of contig in original sense
C
IENDGT = RELPG(IC) + IRADD(JCON) - WINDOW + IENDG
END IF
END IF
IENDCT = IENDC - ILADD(MCON)
WRITE(IDEV,*)
+ ' Possible join between contig ',JCONN,' in the ',
+ STRAND,' sense and contig ',NCON
WRITE(IDEV,1000)X
1000 FORMAT(' Percentage mismatch after alignment = ',F4.1)
WRITE(NAME1,1002)JCONN
WRITE(NAME2,1002)NCON
1002 FORMAT(I6)
CALL FMT4LP(SEQC2(1),SEQG2(IENDG),LO,IENDCT,IENDGT,IDEV,
+ NAME2,NAME1)
NFOUND = NFOUND + 1
END IF
IFAIL=0
END
SUBROUTINE ADISM5(IDIM,IDIMG,SAVPS,SAVPG,IDSAV,
+CENDS,NENDS,IDCEND,MAXCON,ILEFTS,ILC,IPOSC,IPOSG,ISENSE,
+LLINO,IMATC,ISTRAN,MAXC,KBOUT,MCON)
C AUTHOR: RODGER STADEN
INTEGER ILEFTS(MAXC),ILC(MAXC),IPOSC(MAXC),IPOSG(MAXC)
INTEGER ISENSE(MAXC),LLINO(MAXC),MCON(MAXC)
INTEGER CENDS(MAXCON)
INTEGER NENDS(MAXCON)
INTEGER SAVPS(IDSAV),SAVPG(IDSAV)
NEXTC=IDIM+1
CALL BUB2AS(SAVPS,SAVPG,IDSAV)
IMATC=IMATC+1
CALL ADISM6(SAVPS(1),SAVPG(1),CENDS,NENDS,IDCEND,MAXCON,
+ ILEFTS,ILC,IPOSC,IPOSG,ISENSE,LLINO,IMATC,ISTRAN,NEXTC,MAXC,
+ KBOUT,MCON)
LEND=IDIMG-SAVPG(1)+SAVPS(1)
DO 10 I=2,IDSAV
IF((SAVPS(I).LT.LEND).AND.(SAVPS(I).LT.NEXTC))GO TO 10
IMATC=IMATC+1
CALL ADISM6(SAVPS(I),SAVPG(I),CENDS,NENDS,IDCEND,MAXCON,
+ ILEFTS,ILC,IPOSC,IPOSG,ISENSE,LLINO,IMATC,ISTRAN,NEXTC,MAXC,
+ KBOUT,MCON)
LEND=IDIMG-SAVPG(I)+SAVPS(I)
10 CONTINUE
IMATC = MIN(IMATC,MAXC)
END
SUBROUTINE ADISM6(ISAVPS,SAVPG,CENDS,NENDS,
+IDCEND,MAXCON,ILEFTS,ILC,IPOSC,IPOSG,ISENSE,LLINO,IMATC,ISTRAN,
+NEXTC,MAXC,KBOUT,MCON)
C AUTHOR: RODGER STADEN
INTEGER ILEFTS(MAXC),ILC(MAXC),IPOSC(MAXC),IPOSG(MAXC)
INTEGER ISENSE(MAXC),LLINO(MAXC),MCON(MAXC)
INTEGER SAVPS,SAVPG,CENDS(MAXCON)
INTEGER NENDS(MAXCON)
SAVPS=ISAVPS-19
JJ=1
DO 5 J=2,IDCEND
IF(SAVPS.GT.CENDS(J))GO TO 5
JJ=J-1
GO TO 6
5 CONTINUE
JJ=IDCEND
6 CONTINUE
C new bit need to save contig number for alinej
SAVPS=SAVPS-1
LCL=SAVPS-CENDS(JJ)
LCR=CENDS(JJ+1)-ISAVPS-1
NEXTC=CENDS(JJ+1)+20
IF(IMATC.LE.MAXC) THEN
MCON(IMATC) = JJ
ILEFTS(IMATC)=CENDS(JJ)+20
ILC(IMATC)=LCL+LCR+1
IPOSC(IMATC)=LCL+1
IPOSG(IMATC)=SAVPG
LLINO(IMATC)=NENDS(JJ)
ISENSE(IMATC)=1
IF(ISTRAN.EQ.2)ISENSE(IMATC)=-1
ELSE
CALL ERROM(KBOUT,'Warning: too many overlaps')
END IF
END
C JCONS
SUBROUTINE JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,IDIM1,GEL,IDBSIZ,ISTART,JOB,LLINO,LINCON,LREG,RREG,TEMP,
+CHRSIZ,MAXGL2,KBOUT,
+IDEVW,IFAIL,MAXGEL,IDM,PERCD,TGEL,ILADD,IRADD,MAXCON,JCON,
+IWIN,NBAD)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),CHRSIZ,ILADD(MAXCON),IRADD(MAXCON)
INTEGER LREG,RREG,X,Y,TEMP(CHRSIZ,MAXGL2)
CHARACTER SEQ1(IDIM1)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL),TGEL(MAXGEL)
CHARACTER NAMPRO*(*)
CALL BUSY(KBOUT)
C WRITE(*,*)'NGELS,NCONTS,IDIM1,ISTART,LREG,RREG'
C WRITE(*,*)NGELS,NCONTS,IDIM1,ISTART,LREG,RREG
C JOB = 0 do all contigs, = 1 do one contig llino,lincon
IFAIL=0
IF (JOB.EQ.0) THEN
N=IDBSIZ-NCONTS
NCONS = 0
DO 110 I=N,IDBSIZ-1
J=LNBR(I)
X=1
Y=RELPG(I)
ISTART=ISTART+1
IF((ISTART+19+Y+2*MAXGEL).GT.IDIM1)THEN
WRITE(KBOUT,1009)IDIM1
1009 FORMAT(
+ ' Maximum consensus length(',I6,') exceeded',/,
+ ' calculation aborted')
IFAIL=1
RETURN
END IF
CALL ADDTIT(SEQ1(ISTART),NAMPRO,J,ISTART)
NCONS = NCONS + 1
IDIN = 0
IF(IWIN.GT.0) THEN
IDIN = MAXGEL
CALL GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,I,1,
+ GEL,TGEL,IDIN,IWIN,NBAD)
IF(IDIN.GT.0)CALL SQCOPY(GEL,SEQ1(ISTART),IDIN)
END IF
ILADD(NCONS) = IDIN
ISTART = ISTART + IDIN
CALL SUMMER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ1(ISTART),Y,GEL,X,Y,J,IDBSIZ,TEMP,CHRSIZ,MAXGL2,IDEVW,
+ MAXGEL,IDM,PERCD)
ISTART=ISTART+Y-1
IDIN = 0
IF(IWIN.GT.0) THEN
IDIN = MAXGEL
CALL GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,I,2,
+ GEL,TGEL,IDIN,IWIN,NBAD)
IF(IDIN.GT.0)CALL SQCOPY(GEL,SEQ1(ISTART+1),IDIN)
END IF
IRADD(NCONS) = IDIN
ISTART = ISTART + IDIN
110 CONTINUE
ELSE
C
C do it for one contig
C
J = LLINO
I = LINCON
X = LREG
Y = RREG
ISTART = ISTART + 1
C WRITE(*,*)
C +'LLINO,LINCON,NCONTS,ISTART',LLINO,LINCON,NCONTS,ISTART
IF((ISTART+19+Y+2*MAXGEL).GT.IDIM1)THEN
WRITE(KBOUT,1009)IDIM1
IFAIL=1
RETURN
END IF
CALL ADDTIT(SEQ1(ISTART),NAMPRO,J,ISTART)
NCONS = NCONTS
IDIN = 0
IF(IWIN.GT.0) THEN
IDIN = MAXGEL
CALL GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,I,1,
+ GEL,TGEL,IDIN,IWIN,NBAD)
IF(IDIN.GT.0)CALL SQCOPY(GEL,SEQ1(ISTART),IDIN)
END IF
C WRITE(*,*)'ILADD(JCON)',IDIN
ILADD(JCON) = IDIN
ISTART = ISTART + IDIN
CALL SUMMER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ1(ISTART),Y,GEL,X,Y,J,IDBSIZ,TEMP,CHRSIZ,MAXGL2,
+ IDEVW,MAXGEL,IDM,PERCD)
C repleced by next line 26-1-93 ISTART = ISTART + Y - 1
ISTART = ISTART + RREG - LREG
IDIN = 0
IF(IWIN.GT.0) THEN
IDIN = MAXGEL
CALL GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,I,2,
+ GEL,TGEL,IDIN,IWIN,NBAD)
IF(IDIN.GT.0)CALL SQCOPY(GEL,SEQ1(ISTART+1),IDIN)
END IF
C WRITE(*,*)'IRADD(JCON)',IDIN
IRADD(JCON) = IDIN
ISTART = ISTART + IDIN
END IF
END
SUBROUTINE GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,ICONT,IEND,
+GEL,GELT,ID,IWIN,NBAD)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ),RELPG(IDBSIZ)
CHARACTER GEL(ID),GELT(ID)
EXTERNAL NOK2
MAXGEL = ID
IDT = 0
C routine to find a possible extension to a contig by looking in a tag file
C contig ICONT end IEND = 1 =left 2=right
C return data in GEL, of length ID
C The worst aspect of this is that if we dont choose the very end reading
C we dont know where it lies relative to the consensus. For now just assume
C there are no length difference between the extension and the consensus
C and just add it on the end
IF(IEND.EQ.1) THEN
LMOST = 1
IGEL = LNBR(ICONT)
10 CONTINUE
IF(IGEL.EQ.0) GO TO 100
IF(RELPG(IGEL).GT.MAXGEL) GO TO 100
IF(LNGTHG(IGEL).LT.0) THEN
ID = MAXGEL
CALL GETEXT(IGEL,GELT,ID,IOK)
IF(IOK.EQ.0) THEN
C look for number of n's here and change id accordingly
K = NOK2(GELT,ID,IWIN,NBAD)
LT = MIN(LMOST,RELPG(IGEL)-K)
IF(LT.LT.LMOST) THEN
IS = RELPG(IGEL)
N = K - IS + 1
CALL SQCOPY(GELT(IS),GEL,N)
CALL SQREV(GEL,N)
CALL SQCOM(GEL,N)
IDT = N
LMOST = LT
END IF
ELSE
C WRITE(*,*)'COCKUP IN GETEXT, gel',IGEL
END IF
END IF
IGEL = RNBR(IGEL)
GO TO 10
ELSE
IGEL = RNBR(ICONT)
LMOST = RELPG(ICONT)
IDC = RELPG(ICONT)
20 CONTINUE
IF(IGEL.EQ.0) GO TO 100
IF(LMOST-RELPG(IGEL).GT.MAXGEL) GO TO 100
IF(LNGTHG(IGEL).GT.0) THEN
ID = MAXGEL
CALL GETEXT(IGEL,GELT,ID,IOK)
IF(IOK.EQ.0) THEN
K = NOK2(GELT,ID,IWIN,NBAD)
LT = MAX(LMOST,RELPG(IGEL)+LNGTHG(IGEL)+K-1)
IF(LT.GT.LMOST) THEN
IS = RELPG(ICONT) - (RELPG(IGEL) + LNGTHG(IGEL)) + 2
N = K - IS + 1
CALL SQCOPY(GELT(IS),GEL,N)
IDT = N
LMOST = LT
END IF
ELSE
C WRITE(*,*)'COCKUP IN GETEXT, GEL',IGEL
END IF
END IF
IGEL = LNBR(IGEL)
GO TO 20
END IF
100 CONTINUE
ID = IDT
END
INTEGER FUNCTION NOK2(GEL,ID,IWIN,NBADIN)
CHARACTER GEL(ID)
PARAMETER (MAXPOS = 101)
INTEGER POSNS(MAXPOS),R
EXTERNAL KWRAP
C count N's over a window of iwin, return position
C when over NBAD
C INIT
NBAD = NBADIN + 1
I = 0
N = 0
NOK2 = ID
L = 1
R = 0
IF(NBAD.GT.MAXPOS)THEN
WRITE(*,*)'Scream: nok2 not happy'
RETURN
END IF
10 CONTINUE
I = I + 1
IF(I.GT.ID) RETURN
IF(GEL(I).EQ.'-') THEN
N = N + 1
R = KWRAP(R,NBAD)
POSNS(R) = I
IF(N.GE.NBAD) THEN
IF(POSNS(R)-POSNS(L)+1.LT.IWIN) THEN
NOK2 = POSNS(L)
RETURN
END IF
L = KWRAP(L,NBAD)
END IF
END IF
GO TO 10
END
INTEGER FUNCTION KWRAP(I,J)
IT = I + 1
IF(IT.GT.J) IT = 1
KWRAP = IT
END
SUBROUTINE PADSHF(RELPG,LNGTHG,LNBR,RNBR,
+READS,IDIM1,LREG,RREG,LLINO,IDBSIZ,FREQS,CHRSIZ,MAXGL2,
+IDEVW,MAXGEL,READPS,READNS,PSTART,NPADS,MXG,PADPOS,MAXP,
+KBOUT)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),CHRSIZ
INTEGER LREG,RREG
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER READS(IDIM1),PAD,DASH
C PARAMETER (MXG = 1000)
C PARAMETER (MAXP = MXG * 20)
INTEGER FREQS(CHRSIZ,MAXGL2),READPS(MXG),READNS(MXG)
INTEGER CR,SHIFTF,READST,PCF,WINS,WINE,PG,PC,PCR,CHNRP1
INTEGER PADPOS(MAXP),PSTART(MXG),NPADS(MXG),PADST,PGE
LOGICAL FIRSTP,PASS1
EXTERNAL INDEXS,CHNRP1,NSAMPL
SAVE PAD,DASH
DATA PAD/'*'/,DASH/'-'/
C
C region to process is lreg to rreg
C current active region is wins to wine
C current reading is cr
C we process all the readings covering wins to wine,
C write them to disk, then move wins and wine, and get the first
C reading that covers them, etc
C we save readings in reads and their numbers in readns
C and their start positions in reads in readps
C we accumulate frequencies in freqs
C
NEDITS = 0
NSWAPT = 0
INDPAD = INDEXS(PAD,JUNK)
WINS = LREG
WINE = MIN(WINS + MAXGL2 - 1,RREG)
1 CONTINUE
CR = CHNRP1(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,
+ LLINO,WINS)
IF (CR.EQ.0) RETURN
DO 10 I = 1,MAXGL2
DO 10 J = 1,CHRSIZ
FREQS(J,I) = 0
10 CONTINUE
NREADS = 0
READST = 1
PADST = 1
PASS1 = .TRUE.
20 CONTINUE
CALL READW(IDEVW,CR,READS(READST),MAXGEL)
IF (NREADS.EQ.MXG) THEN
CALL ERROM(KBOUT,'Too many reads for buffer')
RETURN
END IF
NREADS = NREADS + 1
READNS(NREADS) = CR
READPS(NREADS) = READST
READST = READST + ABS(LNGTHG(CR))
SHIFTF = RELPG(CR) - WINS
DO 30 I = MAX(1,WINS-RELPG(CR) + 1),
+ MIN(ABS(LNGTHG(CR)),WINE-RELPG(CR)+1)
JJ = INDEXS(READS(READPS(NREADS)+I-1),JSCORE)
JJJ = SHIFTF + I
FREQS(JJ,JJJ) = FREQS(JJ,JJJ) + 1
30 CONTINUE
IF (RNBR(CR).NE.0) THEN
CR = RNBR(CR)
IF (RELPG(CR).LE.WINE) GO TO 20
END IF
DO 35 I=1,NREADS
NPADS(I) = 0
35 CONTINUE
40 CONTINUE
NSWAP = 0
C pg is position in reading ir
C PCR is position in reads
C pc is position in contig
C pcf is position in freqs
C
C we swap if chars to left and right are not already pads and
C theres at least one of the char to the left in the current column
C or the char to the left is a dash (not always beneficial) and
C the pads are not already aligned with only 1 other symbol
C
C we put the element number of the first pad for each reading at padst
C we count the number of pads in npads
C we store the pad positions in padpos
C
DO 60 IR = 1,NREADS
SHIFTF = WINS - 1
FIRSTP = .TRUE.
DO 50 PG = MAX(2,WINS-RELPG(READNS(IR))+2),
+ MIN(ABS(LNGTHG(READNS(IR))),WINE-RELPG(READNS(IR))+1)
PCR = PG + READPS(IR) - 1
C
C horrible exception for case where base 1 in read is pad
C we wont see it this pass but will when we write out tags
C so make sure we do see it now or we cockup later
C
IF (PASS1) THEN
IF (PG.EQ.2) THEN
IF (READS(PCR-1).EQ.PAD) THEN
PSTART(IR) = PADST
NPADS(IR) = NPADS(IR) + 1
PADPOS(PADST) = PG - 1
IF (PADST.EQ.MAXP) THEN
CALL ERROM(KBOUT,'Too many pads for buffer')
RETURN
END IF
PADST = PADST + 1
FIRSTP = .FALSE.
END IF
END IF
END IF
IF (READS(PCR).EQ.PAD) THEN
IF (PASS1) THEN
IF (FIRSTP) PSTART(IR) = PADST
NPADS(IR) = NPADS(IR) + 1
PADPOS(PADST) = PG
IF (PADST.EQ.MAXP) THEN
CALL ERROM(KBOUT,'Too many pads for buffer')
RETURN
END IF
PADST = PADST + 1
FIRSTP = .FALSE.
END IF
PC = PG + RELPG(READNS(IR)) - 1
INPCRM = INDEXS(READS(PCR-1),JSCORM)
IF (INPCRM.NE.INDPAD) THEN
PCF = PC - SHIFTF
IF (((FREQS(INPCRM,PCF).NE.0).OR.
+ (READS(PCR-1).EQ.DASH)).AND.
+ (FREQS(INDPAD,PCF).LT.(NSAMPL(FREQS(1,PCF),CHRSIZ)-1)))
+ THEN
C
C swap
C
READS(PCR) = READS(PCR-1)
READS(PCR-1) = PAD
INPCR = INDEXS(READS(PCR),JSCORE)
FREQS(INPCRM,PCF-1) = FREQS(INPCRM,PCF-1) - 1
FREQS(INPCR,PCF) = FREQS(INPCR,PCF) - 1
FREQS(INPCR,PCF-1) = FREQS(INPCR,PCF-1) + 1
FREQS(INPCRM,PCF) = FREQS(INPCRM,PCF) + 1
NSWAP = NSWAP + 1
END IF
END IF
END IF
50 CONTINUE
60 CONTINUE
C WRITE(*,*)'NUMBER OF SWAPS',NSWAP
NSWAPT = NSWAPT + NSWAP
PASS1 = .FALSE.
IF (NSWAP.GT.0) GO TO 40
C
C no more movement so write back wot weve changed so far
C
DO 70 IR = 1,NREADS
K = 0
NPAD = 0
DO 65 PG = MAX(1,WINS-RELPG(READNS(IR))+1),
+ MIN(ABS(LNGTHG(READNS(IR))),WINE-RELPG(READNS(IR))+1)
PCR = PG + READPS(IR) - 1
IF (READS(PCR).EQ.PAD) THEN
L = PADPOS(PSTART(IR)+NPAD)
IF (PG.LT.L) THEN
PC = PG + RELPG(READNS(IR)) - 1
LE = L
PGE = PG
IF (LNGTHG(READNS(IR)).LT.0) THEN
LE = 1 - LNGTHG(READNS(IR)) - LE
PGE = 1 - LNGTHG(READNS(IR)) - PGE
C WRITE(*,*)READNS(IR),' insert at',PGE,PC,' del at',LE
CALL DELEDT(READNS(IR),LE,'*')
CALL INSEDT(READNS(IR),PGE,'*')
ELSE
C WRITE(*,*)READNS(IR),' del at',LE,' insert at',PGE,PC
CALL DELEDT(READNS(IR),LE,'*')
CALL INSEDT(READNS(IR),PGE,'*')
END IF
NEDITS = NEDITS + 1
END IF
NPAD = NPAD + 1
END IF
65 CONTINUE
CALL WRITEW(IDEVW,READNS(IR),READS(READPS(IR)),MAXGEL)
70 CONTINUE
C
C we allow the next chunk to overlap the previous one by 20
C in case some pads at the right edge of it could still move
C further left. Alternatively we could look for 2 adjacent
C positions which have 100% consensus and are different
C
IF (WINE.NE.RREG) THEN
WINS = MAX(LREG,WINE-19)
WINE = MIN(WINS + MAXGL2 - 1,RREG)
GO TO 1
END IF
C WRITE(*,*)'Total swaps',NSWAPT
WRITE(KBOUT,*)'Number of pads moved',NEDITS
END
INTEGER FUNCTION NSAMPL(COUNTS,IDM)
C
C count the number of reads covering this position
C
INTEGER IDM
INTEGER COUNTS(IDM)
ISUM = 0
DO 5 I=1,IDM
ISUM = ISUM + COUNTS(I)
5 CONTINUE
NSAMPL = ISUM
END
INTEGER FUNCTION CONOK(
+RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ,MAXSEQ,SEQ2,IDBSIZ,TEMP3,
+ECHRSZ,MAXGL2,KBOUT,IDEVW,IDEV,
+MAXGEL,IDM,PERCD,CENDS,NENDS,MAXCON)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER ECHRSZ,TEMP3(ECHRSZ,MAXGL2),CENDS(MAXCON),NENDS(MAXCON)
CHARACTER SEQ(MAXSEQ),SEQ2(MAXGEL),NAMPRO*(*)
EXTERNAL NOK2
C
C routine to calc a consensus and look for ibad dashes in iwin bases
C
C returns number of cocked-up contigs or -1 for error in consensus calc
C for each contig it stops where it find the first problem.
C
CONOK = 0
JOB = 0
IDIM1 = 0
CALL ACONSN(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ,MAXSEQ,SEQ2,IDBSIZ,IDIM1,JOB,KDUMM,KDUMM,KDUMM,TEMP3,
+ECHRSZ,MAXGL2,KBOUT,IDEVW,IFAIL,MAXGEL,IDM,PERCD)
IF(IFAIL.NE.0) THEN
CALL ERROM(KBOUT,'Error calculating consensus')
CONOK = -1
RETURN
END IF
CALL FNDCON(SEQ,IDIM1,CENDS,NENDS,IDCEND,MAXCON,KBOUT)
IWIN = 20
NBAD = 15
DO 10 I=1,IDCEND
J = CENDS(I) + 20
IDIM = CENDS(I+1) - J
K = NOK2(SEQ(J),IDIM,IWIN,NBAD)
IF (K.LT.IDIM) THEN
WRITE(IDEV,*)'Problem at position',K,' In contig',NENDS(I)
CONOK = CONOK + 1
END IF
10 CONTINUE
IF (CONOK.EQ.0) THEN
WRITE(KBOUT,*)
+' Consensus has no segments with',NBAD,' dashes in',IWIN
ELSE
WRITE(KBOUT,*)
+ CONOK,' contigs have segments with',NBAD,' dashes in',IWIN
END IF
END
SUBROUTINE AUTOM(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
+NGELS,NCONTS,LLINO,LINCON,MAXGEL,
+TEMP3,SEQ1,MAXSEQ,SEQ2,SEQ5,SEQC2,SEQG2,
+MAXGLM,MAXGL2,ECHRSZ,
+SAV1,SAV2,SAV3,MAXSAV,
+KBIN,KBOUT,IDEV1,IDEV2,IDEV3,IDEV8,IDEV,
+IHELPS,IHELPE,HELPF,IDEVH,NAMARC,NAMPRO,FILE,
+PERCD,IOPEN,IDM,SEQG3,SEQC3,IOK,IDEVC,IDEVT)
INTEGER ECHRSZ,SELCON
INTEGER RELPG(MAXDB)
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
INTEGER TEMP3(ECHRSZ,MAXGL2)
CHARACTER SEQC2(MAXGLM,2),SEQG2(MAXGLM,2)
CHARACTER SEQ1(MAXSEQ),SEQ2(MAXGLM)
INTEGER SAV1(MAXSAV),SAV2(MAXSAV),SAV3(MAXSAV)
CHARACTER NAMARC*(*),NAMPRO*(*),FILE*(*)
CHARACTER SEQ5(MAXGLM),HELPF*(*),SEQG3(MAXGLM),SEQC3(MAXGLM)
C
C take the poor data from reads to see if it aligns with the consensus
C
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ TEMP3,IERR,KBOUT)
IF(IERR.GT.1) RETURN
IFAIL = 0
IF(NGELS.LT.1) RETURN
C MN = 0
C MX = 50
C MAXPG = 20
C CALL GETINT(MN,MX,MAXPG,
C +'Maximum pads per sequence',
C +IVAL,KBIN,KBOUT,
C +IHELPS,IHELPE,HELPF,IDEVH,IOK)
C IF(IOK.NE.0) RETURN
MAXPG = IVAL
MAXPC = IVAL
RMN = 0.
RMX = 100.
PERMAX = 13.
CALL GETRL(RMN,RMX,PERMAX,
+ 'Maximum percent mismatch after alignment',
+ VAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
PERMAX = VAL
MN = 1
MX = MAXGEL
IWING = 100
CALL GETINT(MN,MX,IWING,
+ 'Window size for good data scan',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
IWING = IVAL
MN = 1
MX = MIN(100,IWING)
NBAD = MIN(IWING,5)
CALL GETINT(MN,MX,NBAD,
+ 'Maximum number of dashes in scan window',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
NBAD = IVAL
CALL YESNO(IREPN,'Save failed names in a file',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF (IREPN.LT.0) RETURN
IF (IREPN.EQ.0) THEN
CALL OPENF1(IDEV8,FILE,1,IOK,KBIN,KBOUT,
+ 'File for names of failed reads',
+ IHELPS,IHELPE,HELPF,IDEVH)
IF (IOK.NE.0) RETURN
END IF
CALL YESNO(SELCON,'Select contigs',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(SELCON.LT.0) GO TO 100
IF(SELCON.EQ.0) THEN
CALL GETLN3(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
+ LLINO,NULGEL,IOK,IDBSIZ,KBIN,KBOUT,IDEV3,
+ 'Contig identifier',
+ IHELPS,IHELPE,HELPF,IDEVH)
IF(IOK.NE.0) GO TO 100
CALL GETREG(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ 1,RELPG(LINCON),LREG,RREG,LINCON,LLINO,IDBSIZ,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) GO TO 100
END IF
IDIM2=MAXGEL
CALL AUTOMN(SEQ1,MAXSEQ,SEQ2,IDIM2,
+LLINO,LINCON,IFCOMP,LREG,RREG,
+IDEV,MAXGEL,MAXGLM,
+SAV1,SAV2,SAV3,MAXSAV,
+SEQG2,SEQC2,
+PERMAX,SEQG3,SEQC3,
+RELPG,LNBR,IDBSIZ,NGELS,NCONTS,
+LNGTHG,RNBR,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,PERCD,IWING,NBAD,
+ECHRSZ,TEMP3,MAXGL2,IDM,NAMPRO,KBIN,KBOUT,SELCON,IREPN,IDEV8,
+IHELPS,IHELPE,HELPF,IDEVH)
100 CONTINUE
IF(IREPN.EQ.0) CLOSE(UNIT=IDEV8)
END
SUBROUTINE AUTOMN(SEQ1,MAXSEQ,GEL,IDIMGI,
+LLINO,LINCON,IFCOMP,LREG,RREG,
+IDEV,MAXGEL,MAXGLM,
+SAVPS,SAVPG,SAVL,MAXSAV,
+SEQG2,SEQC2,
+PERMAX,SEQG3,SEQC3,
+RELPG,LNBR,IDBSIZ,NGELS,NCONTS,
+LNGTHG,RNBR,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,PERCD,IWING,NBAD,
+ECHRSZ,TEMP3,MAXGL2,IDM,NAMPRO,KBIN,KBOUT,SELCON,IREPN,IDEV8,
+IHELPS,IHELPE,HELPF,IDEVH)
C AUTHOR: RODGER STADEN
INTEGER ECHRSZ
INTEGER SAVPS(MAXSAV),SAVPG(MAXSAV),SAVL(MAXSAV)
CHARACTER NAMPRO*(*),HELPF*(*)
CHARACTER SEQ1(MAXSEQ),GEL(MAXGLM)
CHARACTER SEQG2(MAXGLM,2),SEQC2(MAXGLM,2)
CHARACTER SEQG3(MAXGLM),SEQC3(MAXGLM)
CHARACTER NAMT*16
PARAMETER (MAXCON = 1,MING = 10,MAXG = 500)
INTEGER ILADD(MAXCON),IRADD(MAXCON)
INTEGER RREG,FIRSTR,SELCON,FIRSTC
INTEGER RELPG(IDBSIZ),LNBR(IDBSIZ),LNGTHG(IDBSIZ),RNBR(IDBSIZ)
INTEGER TEMP3(ECHRSZ,MAXGL2)
INTEGER CHNRP1,XVERSN
EXTERNAL CHNRP1,XVERSN,NOK2
JOB = 1
JCON = 1
NPROBS = 0
IF (SELCON.EQ.0) THEN
FIRSTC = LINCON
LASTC = LINCON
ELSE IF (SELCON.EQ.1) THEN
FIRSTC = IDBSIZ-NCONTS
LASTC = IDBSIZ-1
ELSE
CALL ERROM(KBOUT,'Error in AUTOM: unexpected option')
RETURN
END IF
DO 50 ICONT = FIRSTC,LASTC
IF (SELCON.EQ.1) THEN
LINCON = ICONT
LLINO = LNBR(LINCON)
LREG = 1
RREG = RELPG(LINCON)
END IF
IDIM = 0
CALL JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+ SEQ1,MAXSEQ,GEL,IDBSIZ,IDIM,JOB,LLINO,LINCON,LREG,RREG,
+ TEMP3,
+ ECHRSZ,MAXGL2,KBOUT,IDEV2,IOK,MAXGEL,IDM,PERCD,SEQG3,
+ ILADD,IRADD,MAXCON,JCON,0,NBAD)
IF (IOK.NE.0) RETURN
C CALL FMTDB(SEQ1,IDIM,1,IDIM,60,KBOUT)
LENCON = RREG - LREG + 1
ISTRAN = 1
5 CONTINUE
C
C main loop
C
FIRSTR = CHNRP1(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,
+ LNBR(LINCON),LREG)
IF(FIRSTR.EQ.0) GO TO 50
IRNO = FIRSTR
10 CONTINUE
IF (LNGTHG(IRNO).GT.0) THEN
IDIN = MIN(MAXG-LNGTHG(IRNO)+1,MAXGLM)
IF(IDIN.GT.MING) THEN
CALL GETEXT(IRNO,GEL,IDIN,IOK)
IF(IOK.EQ.0) THEN
K = NOK2(GEL,IDIN,IWING,NBAD)
IDIN = K
ELSE
IDIN = 0
END IF
ELSE
IDIN = 0
END IF
C
C fudge idin (it seems to return 1 less char than its value!)
C
IDIN = IDIN - 2
C WRITE(*,*)'IDIN',IDIN
IF(IDIN.GT.MING) THEN
C
C trim gel if it goes off the end of the consensus!
C
IDIN = MIN((LENCON-(RELPG(IRNO)+LNGTHG(IRNO)-1)),IDIN)
C CALL FMTDB(GEL,IDIN,1,IDIN,60,KBOUT)
JDIM22 = IDIN
JDOUT = MAXGEL
IDSAV = MAXSAV
JPOSC = RELPG(IRNO)+LNGTHG(IRNO) - LREG + 1
LC = LENCON - JPOSC + 1
IPC = RELPG(IRNO) + LNGTHG(IRNO) - 1
C
C fudge the consensus position as we dont seem to get alignments for
C cases where a deletion is required at the start of the consensus
C
C CALL ALINEM(SEQ1(20+JPOSC),GEL,SEQG3,SEQC3,
CALL ALINEM(SEQ1(18+JPOSC),GEL,SEQG3,SEQC3,
+ SAVPS,SAVPG,SAVL,IDSAV,LC,JDIM22,JDOUT,
+ 1,1,
+ JFAIL,PERMAX,KBOUT,IDEV,
+ MAXGEL,PERMS,IPC,IRNO,LNBR(LINCON),IFAIL)
IF (IFAIL.EQ.0) THEN
IF (JFAIL.NE.0) NPROBS = NPROBS + 1
IF ((JFAIL.NE.0).AND.(IREPN.EQ.0)) THEN
CALL READN(IDEV3,IRNO,NAMT)
WRITE(IDEV8,1000)NAMT,IRNO,LLINO,IPC
1000 FORMAT(' ',A,' ',3I6)
END IF
IF((JFAIL.NE.0).AND.(XVERSN().NE.0).AND.(IDEV.EQ.KBOUT))
+ THEN
CALL BPAUSE(KBIN,KBOUT,IOK)
IF (IOK.NE.0) GO TO 100
CALL YESNO(IJOIN,'Use the editor',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(IJOIN.LT.0) GO TO 100
IF (IJOIN.EQ.0) THEN
CALL CXEDIT(IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,
+ RELPG,LNGTHG,LNBR,RNBR,MAXGEL,
+ IDBSIZ,LINCON,LNBR(LINCON),IRNO,LNGTHG(IRNO),
+ PERCD,IDM,1,IOK)
END IF
CALL BUSY(KBOUT)
END IF
END IF
END IF
END IF
IRNO = RNBR(IRNO)
IF(IRNO.NE.0) THEN
IF((RELPG(IRNO)+LNGTHG(IRNO)).LT.RREG) GO TO 10
END IF
IF (ISTRAN.EQ.1) THEN
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
+ LNBR(LINCON),GEL,IDBSIZ,KBOUT,IDEV1,IDEV2,MAXGEL)
LREG = RELPG(LINCON) - RREG + 1
RREG = LREG + LENCON - 1
CALL SQREV(SEQ1(21),LENCON)
CALL SQCOM(SEQ1(21),LENCON)
ISTRAN = 2
GO TO 5
END IF
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
+ LNBR(LINCON),GEL,IDBSIZ,KBOUT,IDEV1,IDEV2,MAXGEL)
ISTRAN = 3
50 CONTINUE
100 CONTINUE
WRITE(KBOUT,*)'Number of possible problems ',NPROBS
C
C if required return the contig to original sense
C
IF (ISTRAN.EQ.2) THEN
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
+ LNBR(LINCON),GEL,IDBSIZ,KBOUT,IDEV1,IDEV2,MAXGEL)
END IF
END
SUBROUTINE ALINEM(SEQ1,SEQ2,SEQG2,SEQC2,ISAV1,ISAV2,ISAV3,
+IDSAV,IDC,IDIM2,IDOUT,IC1,IG1,
+IFAIL,PERMAX,KBOUT,IDEV,MAXGEL,PERCM,IPC,IRNO,LLINO,JFAIL)
C AUTHOR: RODGER STADEN
CHARACTER SEQ1(IDC),SEQ2(IDIM2),SEQG2(IDOUT),SEQC2(IDOUT)
INTEGER ISAV1(IDSAV),ISAV2(IDSAV),ISAV3(IDSAV)
C INTEGER PATH(5000)
CHARACTER NAME1*6,NAME2*6
PARAMETER (MINOVR = 10, MINSLT = 3)
EXTERNAL PMIS
C
C the crap must be at least minovr bases in length or we dont bother
C
JFAIL = 1
IF((IDC.LT.MINOVR).OR.(IDIM2.LT.MINOVR)) RETURN
WRITE(NAME1,1002)LLINO
WRITE(NAME2,1002)IRNO
1002 FORMAT(I6)
NAME1(1:1) = 'C'
NAME2(1:1) = 'R'
IDC1 = MIN(IDC,IDIM2)
X = MAX(1.0,REAL(IDC1)/100.)
C
C allowing 10% and 7% of overlap to be pads: consensus and read respectively
C
MAXPC = NINT(10.0*X)
MAXPG = NINT(7.0*X)
IPP=IDSAV
CALL SLIDER(SEQ1,IDC,SEQ2,IDIM2,IC1,IG1,MAXPG,MAXPC,MINSLT,
+ISAV1,ISAV2,ISAV3,IPP)
IF((IPP.GT.IDSAV).OR.(IPP.LT.1)) THEN
CALL ERROM(KBOUT,'Warning: slider failed')
CALL ERROM(KBOUT,NAME2)
RETURN
END IF
CALL REMOVL(ISAV2,ISAV3,ISAV1,IPP)
CALL BUB3AS(ISAV2,ISAV3,ISAV1,IPP)
CALL TPCHEK(ISAV2,ISAV3,ISAV1,IPP)
CALL UPCHEK(ISAV2,ISAV3,ISAV1,IPP)
CALL LINEUP(SEQ2,SEQ1,SEQG2,SEQC2,IDC,IDIM2,IDOUT,ISAV3,ISAV2,
+ISAV1,IPP,ITOTPC,ITOTPG,JOINT,ITYPE,KBOUT,MAXGEL,JFAIL)
IF(JFAIL.NE.0) THEN
CALL ERROM(KBOUT,'Warning: lineup failed')
CALL ERROM(KBOUT,NAME2)
RETURN
END IF
C IDC1 = MIN(IDC,IDIM2+MAX(MAXPG,MAXPC))
C IDC1 = MIN(IDC,IDIM2)
C WRITE(*,*)'IDC,IDIM2',IDC,IDIM2
C MMAXPC = -1*(MAXPC+MAXPC/2)
C X = MAX(1.0,REAL(IDC1)/100.)
C MMAXPC = NINT(-10.*X)
C MMAXPG = NINT(7.*X)
C MAXPC = -MMAXPC
C MAXPG = MMAXPG
C IDIM3 = IDC1
C WRITE(*,*)'PADS ALLOWED',MAXPC,MAXPG
C CALL GALIGN(SEQ1,IDC1,SEQ2,IDIM3,MMAXPC,MMAXPG,PATH)
C CALL DISP(SEQ1,IDC1,SEQ2,IDIM3,PATH)
C CALL EXPAND(SEQ1,IDC1,SEQ2,IDIM3,SEQC2,IDC2,SEQG2,IDG2,PATH)
C LO = MIN(IDC2,IDG2)
C WRITE(*,*)'IDC2,IDG2',IDC2,IDG2
C LO = MIN(NOTIRL(SEQC2,IDC2,','),NOTIRL(SEQG2,IDG2,','))
C WRITE(*,*)'LO',LO
C END IF
LO = MIN(IDOUT,IDIM2)
PERCM = PMIS(SEQC2,SEQG2,LO)
ITOTPC = NSYM(SEQC2,LO,',')
ITOTPG = NSYM(SEQG2,LO,',')
IFAIL = 0
IF (ITOTPC.GT.MAXPC) IFAIL = 1
IF (ITOTPG.GT.MAXPG) IFAIL = 1
IF (PERCM.GT.PERMAX) IFAIL = 1
IF(IFAIL.NE.0) THEN
WRITE(IDEV,1000)PERCM,ITOTPC,ITOTPG
1000 FORMAT(' Percentage mismatch ',F4.1,', Pads',I4,I4)
CALL FMT4LP(SEQC2(1),SEQG2,LO,IPC,1,IDEV,
+ NAME1,NAME2)
CALL BUSY(KBOUT)
END IF
END
INTEGER FUNCTION NSYM(SEQ,ID,SYM)
CHARACTER SEQ(ID),SYM
N = 0
DO 10 I=1,ID
IF(SEQ(I).EQ.SYM) N = N + 1
10 CONTINUE
NSYM = N
END
REAL FUNCTION PMIS(SEQ1,SEQ2,ID)
CHARACTER SEQ1(ID),SEQ2(ID),PAD
PARAMETER (PAD = ',')
C
C count mismatch. padding in consensus ignored
C
J = 0
DO 10 I=1,ID
IF(SEQ1(I).NE.SEQ2(I)) THEN
IF(SEQ1(I).NE.PAD) J = J + 1
END IF
C IF(SEQ1(I).NE.SEQ2(I)) J = J + 1
10 CONTINUE
PMIS = 100. * REAL(J)/REAL(ID)
END
SUBROUTINE UPCHEK(PC,PG,L,N)
INTEGER PC(N),PG(N),L(N),DC,DG
C AUTHOR RODGER STADEN
C
C only allow gaps that are shorter than the next block of identity
C
K1 = 2
1 CONTINUE
DO 10 I = K1,N
J1 = I
DC = PC(I) - PC(I-1) - L(I-1)
DG = PG(I) - PG(I-1) - L(I-1)
IF(ABS(DC-DG).GE.L(I)) GO TO 20
10 CONTINUE
RETURN
20 CONTINUE
C WRITE(*,*)'REMOVING!!'
CALL ML(PC,PG,L,N,J1)
C IF(L(J1-1).GT.L(J1)) THEN
C CALL ML(PC,PG,L,N,J1)
C ELSE
C CALL ML(PC,PG,L,N,J1-1)
C END IF
K1 = MAX(2,J1-1)
N = N - 1
GO TO 1
END
SUBROUTINE ARRFIN(IDEV,SEQNCE,J,KBOUT,ICRAP)
CHARACTER TEMP(80),SEQNCE(J)
CHARACTER SPACE,TITCHR,GT
EXTERNAL NOK2
SAVE SPACE,TITCHR,GT
PARAMETER (IWIN = 100, NBAD = 5)
DATA SPACE/' '/
DATA TITCHR/';'/
DATA GT/'>'/
C
C routine to read reads, including their poor data if required
C allowing 5 n's in 100 bases
C
IDMX=J
J=0
1 CONTINUE
READ(IDEV,1001,END=30,ERR=80)TEMP
1001 FORMAT(80A1)
IF(TEMP(1).EQ.TITCHR) GO TO 1
DO 20 I=1,80
IF(TEMP(I).NE.SPACE)THEN
IF(J.EQ.IDMX)THEN
CALL ERROM(KBOUT,'Error in arrfin: too much data')
RETURN
END IF
J=J+1
SEQNCE(J)=TEMP(I)
END IF
20 CONTINUE
GO TO 1
30 CONTINUE
C WRITE(*,*)' GOOD',J
IF(ICRAP.NE.0) RETURN
C
C read in the crap
C
REWIND(IDEV)
JG = J
50 CONTINUE
READ(IDEV,1001,END=70,ERR=80)TEMP
IF(TEMP(1).NE.TITCHR) GO TO 50
IF(TEMP(2).EQ.GT) THEN
DO 60 I=3,80
IF(TEMP(I).NE.SPACE)THEN
IF(J.EQ.IDMX)THEN
CALL ERROM(KBOUT,'Error in arrfin: too much data')
GO TO 70
END IF
J=J+1
SEQNCE(J)=TEMP(I)
END IF
60 CONTINUE
END IF
GO TO 50
70 CONTINUE
C WRITE(*,*)' GOOD+BAD',J
K = NOK2(SEQNCE(JG+1),J-JG+1,IWIN,NBAD)
J = JG + K
C WRITE(*,*)' GOOD+BAD-CRAP',J
C WRITE(*,*)(SEQNCE(K),K=1,J)
RETURN
80 CONTINUE
CALL ERROM(KBOUT,'Error reading file in arrfin')
J = 0
END
SUBROUTINE DBLSTR(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,SEQ1,
+IDIM1,GEL,IDBSIZ,TEMP3,ID1,CHRSIZ,MAXGL2,KBIN,KBOUT,IDEVW,
+IDEVR,IDEV,LINLEN,PERCD,
+IHELPS,IHELPE,FILEH,IDEVH,MAXGEL,IDEVN,
+ LLINO,LINCON,LREG,RREG,MXGOOD,SEQ2,IDM,JOB,IERR,LSTRT,LEND)
CHARACTER FILEH*(*)
C AUTHOR: RODGER STADEN
INTEGER RREG, RELPG(IDBSIZ),CHRSIZ
INTEGER LREG,TEMP3(ID1,CHRSIZ,MAXGL2)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL)
CHARACTER SEQ1(IDIM1),SEQ2(IDIM1)
C DBLSTR
C JOB 0 = Ask initial questions
C JOB 1 = Generate quality information
C JOB 2 = Complement contig and region info.
C
IF (JOB.EQ.0) THEN
CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+LINCON,LLINO,IERR,IDBSIZ,KBIN,KBOUT,IDEVN,
+IHELPS,IHELPE,FILEH,IDEVH)
IF(IERR.NE.0) RETURN
CALL GETREG(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+1,RELPG(LINCON),LREG,RREG,LINCON,LLINO,IDBSIZ,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IERR)
IF(IERR.NE.0) RETURN
ELSE IF (JOB.EQ.1) THEN
CALL SUMMAN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQ1,IDIM1,GEL,LSTRT,LEND,LLINO,PERCD,IDBSIZ,
+TEMP3,ID1,CHRSIZ,MAXGL2,IDEVW,
+MAXGEL,MXGOOD)
IDIM1=LEND-LSTRT+1
CALL SUMMER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQ2(LSTRT),IDIM1,GEL,LSTRT,LEND,LLINO,IDBSIZ,TEMP3,
+CHRSIZ,MAXGL2,IDEVW,MAXGEL,IDM,PERCD)
ELSE IF (JOB.EQ.2) THEN
C
C for complementary strand need to juggle the active region
C
LSTRT = LREG-LSTRT
LEND = LREG-LEND
IREG = RREG
RREG = RELPG(LINCON) - LREG + 1
LREG = RELPG(LINCON) - IREG + 1
LSTRT = LREG-LSTRT
LEND = LREG-LEND
IF (LSTRT.LT.1) LSTRT=1
IF (LEND.LT.1) LEND=1
C
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ LINCON,LNBR(LINCON),GEL,IDBSIZ,KBOUT,IDEVR,IDEVW,
+ MAXGEL)
LLINO = LNBR(LINCON)
CALL SUMMAN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ1,IDIM1,GEL,LSTRT,LEND,LLINO,PERCD,IDBSIZ,
+ TEMP3,ID1,CHRSIZ,MAXGL2,IDEVW,
+ MAXGEL,MXGOOD)
CALL SUMMER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2(LSTRT),IDIM1,GEL,LSTRT,LEND,LLINO,IDBSIZ,TEMP3,
+ CHRSIZ,MAXGL2,IDEVW,MAXGEL,IDM,PERCD)
END IF
END
SUBROUTINE SUMMAN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQ1,IDIM1,GEL,LREG,RREG,IGELC,PERCD,IDBSIZ,CHARS,
+ID1,CHRSIZ,MAXGL2,IDEVW,MAXGEL,MXGOOD)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),CHRSIZ
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER SEQ1(IDIM1)
CHARACTER GEL(MAXGEL)
INTEGER LREG,RREG,LSEQNO,POSN,Y,POSN1
INTEGER GELC
INTEGER CHARS(CHRSIZ,ID1,MAXGL2)
CHARACTER SYMS(7,7)
EXTERNAL INDEXS,LWRAPS,IGTCON
SAVE SYMS
DATA SYMS/
+'0','4','4','4','5','5','1',
+'4','0','4','4','5','5','1',
+'4','4','0','4','5','5','1',
+'4','4','4','0','5','5','1',
+'6','6','6','6','3','5','7',
+'6','6','6','6','6','3','7',
+'2','2','2','2','8','8','9'/
C
C codes are: using g = good consensus, b = bad consensus, n = no data
C
C + -
C 0 g g =
C 1 g n
C 2 n g
C 3 b b
C 4 g g !=
C 5 g b
C 6 b g
C 7 b n
C 8 n b
C 9 n n (should never occur!!!)
C
C hard to understand this very old code! rewrite it.
C we have a summing array of twice the length of the longest sequence
C posn is posn in contig of next to write, lseqno is current posn in contig
C we write when lseqno-posn ge the length of the longest seq
POSN=LREG
GELC=IGELC
LINLEN=MAXGEL
LSEQNO=RELPG(GELC)
IEND=0
DO 40 I=1,MAXGL2
DO 40 J=1,ID1
DO 40 K=1,CHRSIZ
CHARS(K,J,I)=0
40 CONTINUE
50 CONTINUE
ISS=1
IF(LNGTHG(GELC).LT.0)ISS=2
CALL READW(IDEVW,GELC,GEL,MAXGEL)
C LOOP FOR RELEVANT ELEMENTS THIS GEL
C only use mxgood characters from start of read
C
IF(ISS.EQ.1) THEN
N = MIN(MXGOOD,ABS(LNGTHG(GELC)))
IF(LSEQNO.LT.LREG)LSEQNO=LREG
IS = LSEQNO-RELPG(GELC)+1
ELSE
C LOOP FOR RELEVANT ELEMENTS THIS GEL
C only use mxgood characters from start of read (right end for these)
C
IREND = RELPG(GELC) - LNGTHG(GELC) + 1
IF (MXGOOD.LT.MAXGEL) THEN
LSEQNO = IREND - MXGOOD + 1
ELSE
LSEQNO = RELPG(GELC)
END IF
LSEQNO = MAX(LSEQNO,LREG)
IS = LSEQNO - RELPG(GELC) + 1
N = ABS(LNGTHG(GELC))
END IF
DO 70 I=IS,N
JJ = INDEXS(GEL(I),JSCORE)
JJJ = LWRAPS(LSEQNO,MAXGL2)
CHARS(JJ,ISS,JJJ) = CHARS(JJ,ISS,JJJ) + JSCORE
LSEQNO = LSEQNO + 1
70 CONTINUE
IF(RNBR(GELC).EQ.0)GO TO 200
GELC=RNBR(GELC)
LSEQNO=RELPG(GELC)
IF(LSEQNO.GT.RREG)GO TO 200
C ENOUGH TO OUTPUT?
Y=LSEQNO-POSN
IF(Y.GE.MAXGEL)GO TO 210
GO TO 50
200 CONTINUE
C SET FLAG TO SHOW END REACHED
IEND=1
LINLEN=MAXGEL
Y=RREG-POSN
IF(Y.LT.MAXGEL)LINLEN=Y+1
210 CONTINUE
C SET POINTER TO SEQ1
POSN1=POSN-1
C PREPARE NEXT SECTION OF CHARS FOR OUTPUT
DO 230 I=1,LINLEN
JJJ = LWRAPS(POSN,MAXGL2)
L1 = IGTCON(CHARS(1,1,JJJ),CHRSIZ,PERCD)
L2 = IGTCON(CHARS(1,2,JJJ),CHRSIZ,PERCD)
POSN1 = POSN1 + 1
SEQ1(POSN1) = SYMS(L2,L1)
DO 250 J=1,CHRSIZ
CHARS(J,1,JJJ)=0
CHARS(J,2,JJJ)=0
250 CONTINUE
POSN=POSN+1
230 CONTINUE
IF(POSN.GT.RREG)RETURN
IF((IEND.EQ.1).AND.(POSN.LE.RREG))GO TO 200
C ANY MORE MAXGEL CHAR LENGTHS TO OUTPUT
Y=LSEQNO-POSN
IF(Y.LT.MAXGEL)GO TO 50
C FINISHED COMPLETELY?
GO TO 210
END
INTEGER FUNCTION IGTCON(COUNTS,IDM,CUT)
INTEGER IDM
INTEGER COUNTS(IDM)
CHARACTER CHARSU
EXTERNAL CHARSU
C
C returns values 1 to 7: 7 means no data, 1-5 means a,c,g,t,*
C 6 means no consensus. if we change gtconc we should change this too
C
IGTCON = 7
ISUM = 0
DO 5 I=1,IDM
ISUM = ISUM + COUNTS(I)
5 CONTINUE
IF(ISUM.EQ.0) RETURN
Y = ISUM
DO 10 I = 1,IDM - 1
X = REAL(COUNTS(I))/Y
IF(X.GE.CUT) THEN
IGTCON = I
RETURN
END IF
10 CONTINUE
IGTCON = 6
END
SUBROUTINE CHKREV(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,NCONTS,
+IDEVN,IDEV,KBIN,KBOUT,DONEIT,MATES,IGELS,DIST,RNAMES)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER DONEIT(IDBSIZ),MATES(IDBSIZ),IGELS(IDBSIZ),DIST(IDBSIZ)
INTEGER GCLIN,DTOEND,CHAINL
CHARACTER*(*) RNAMES(IDBSIZ)
LOGICAL SAMEC
EXTERNAL GCLIN,DTOEND,NMATE,SAMEC,CHAINL
PARAMETER (MAXD = 99999)
C
C need to know which ones have already been mated
C
CALL FILLI(DONEIT,NGELS,0)
CALL FILLI(IGELS,NGELS,0)
CALL FILLI(MATES,NGELS,0)
CALL GNAMES(IDEVN,RNAMES,NGELS)
IGEL = 0
IDONE = 0
10 CONTINUE
IGEL = IGEL + 1
IF (IGEL.EQ.NGELS) THEN
IF (IDONE.GT.0) THEN
CALL SHOWP(DIST,IGELS,MATES,IDONE,RNAMES,RELPG,IDBSIZ,IDEV)
ELSE
WRITE(KBOUT,*)'None found'
END IF
RETURN
END IF
IF (DONEIT(IGEL).EQ.1) GO TO 10
MATE = NMATE(IGEL,NGELS,RNAMES,2)
IF (MATE.EQ.0) GO TO 10
DONEIT(MATE) = 1
IDONE = IDONE + 1
C
C we have a pair igel and mate. deal separately with cases of 1 or 2 contigs
C
IF (SAMEC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,NCONTS,IGEL,MATE))
+ THEN
C
C same contig
C
IF (((LNGTHG(IGEL).GT.0).AND.(LNGTHG(MATE).GT.0)).OR.
+ ((LNGTHG(IGEL).LT.0).AND.(LNGTHG(MATE).LT.0))) THEN
C
C >>>>>>> >>>>>>>>> or <<<<<<<< <<<<<<<<<<
C
IGELS(IDONE) = IGEL
MATES(IDONE) = MATE
DIST(IDONE) = MAXD
C WRITE(KBOUT,*)IGEL,MATE,
C + ' are in the same contig face the same way'
GO TO 10
END IF
IF (LNGTHG(IGEL).GT.0) THEN
IF (RELPG(IGEL).GT.RELPG(MATE)+ABS(LNGTHG(MATE)) -1 ) THEN
C
C <<<<<<<222 111>>>>>>>>
C
IGELS(IDONE) = IGEL
MATES(IDONE) = MATE
DIST(IDONE) = MAXD
C WRITE(KBOUT,*)IGEL,MATE,
C + ' are in the same contig and face away'
ELSE
C
C 111>>>>> <<<<<<222
C
IGELS(IDONE) = IGEL
MATES(IDONE) = MATE
DIST(IDONE) = RELPG(MATE)+ABS(LNGTHG(MATE))-RELPG(IGEL)
C WRITE(KBOUT,*)IGEL,RELPG(IGEL),MATE,RELPG(MATE)
END IF
ELSE
C
C <<<<<<111
C
IF (RELPG(MATE).GT.RELPG(IGEL)+ABS(LNGTHG(IGEL)) -1 ) THEN
C
C <<<<<111 222>>>>>
C
IGELS(IDONE) = IGEL
MATES(IDONE) = MATE
DIST(IDONE) = MAXD
C WRITE(KBOUT,*)IGEL,MATE,
C + ' are in the same contig and face away'
ELSE
C
C >>>>>222 <<<<<111
C
IGELS(IDONE) = IGEL
MATES(IDONE) = MATE
DIST(IDONE) = RELPG(IGEL)+ABS(LNGTHG(IGEL))-RELPG(MATE)
C WRITE(KBOUT,*)'same ',IGEL,RELPG(IGEL),MATE,RELPG(MATE)
END IF
END IF
ELSE
C
C different contigs
C
ICONTL = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,IGEL)
ICONT = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,ICONTL)
MCONTL = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,MATE)
MCONT = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,MCONTL)
LENC1 = RELPG(ICONT)
LENC2 = RELPG(MCONT)
LENI = DTOEND(RELPG(IGEL),LNGTHG(IGEL),LENC1)
LENM = DTOEND(RELPG(MATE),LNGTHG(MATE),LENC2)
LENIM = LENI + LENM
IGELS(IDONE) = -IGEL
MATES(IDONE) = MATE
DIST(IDONE) = LENIM
C WRITE(KBOUT,*)'different contigs',IGEL,MATE,' separation',LENIM
END IF
GO TO 10
END
SUBROUTINE SHOWP(DIST,IGELS,MATES,IDONE,RNAMES,RELPG,IDBSIZ,IDEV)
INTEGER DIST(IDONE),IGELS(IDONE),MATES(IDONE),RELPG(IDBSIZ)
CHARACTER*(*) RNAMES(IDBSIZ)
CALL BUBBL3(DIST,IGELS,MATES,IDONE)
DO 10 I=1,IDONE
IF (IGELS(I).GT.0) THEN
J = ABS(IGELS(I))
WRITE(IDEV,1000)RNAMES(J),J,RELPG(J),DIST(I)
J = MATES(I)
WRITE(IDEV,1000)RNAMES(J),J,RELPG(J),DIST(I)
END IF
10 CONTINUE
DO 20 I=1,IDONE
IF (IGELS(I).LT.1) THEN
J = ABS(IGELS(I))
WRITE(IDEV,1000)RNAMES(J),J,RELPG(J),DIST(I),'*'
J = MATES(I)
WRITE(IDEV,1000)RNAMES(J),J,RELPG(J),DIST(I),'*'
END IF
20 CONTINUE
1000 FORMAT(' ',A,3I6,A)
END
INTEGER FUNCTION DTOEND(RELPG,LNGTHG,LENCON)
INTEGER RELPG
IF (LNGTHG.GT.0) THEN
DTOEND = LENCON - RELPG + 1
ELSE
DTOEND = RELPG + ABS(LNGTHG) - 1
END IF
END
LOGICAL FUNCTION SAMEC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,
+NGELS,NCONTS,IGEL,JGEL)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER CHAINL
EXTERNAL CHAINL
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,IGEL)
J = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,JGEL)
SAMEC = .FALSE.
IF (I.EQ.J) SAMEC = .TRUE.
END
SUBROUTINE GNAMES(IDEVN,RNAMES,NGELS)
CHARACTER*(*) RNAMES(NGELS)
DO 10 I=1,NGELS
CALL READN(IDEVN,I,RNAMES(I))
10 CONTINUE
END
INTEGER FUNCTION NMATE(IGEL,NGELS,RNAMES,JOB)
PARAMETER (NAMLEN = 16)
CHARACTER*(NAMLEN) NAME,NAMEM,RNAMES(NGELS)
C
C assume s1 and r1 are mates
C
C if job = 1 we look at all the names
C if job = 2 we look only at the ones with higher numbers
NMATE = 0
IF(JOB.EQ.1) THEN
JGEL = 1
ELSE IF(JOB.EQ.2) THEN
JGEL = IGEL +1
ELSE
WRITE(*,*)'SCREAM: NMATE'
RETURN
END IF
NAME = RNAMES(IGEL)
I = INDEX(NAME,'.')
IF (NAME(I+1:I+1).EQ.'s') THEN
NAME(I+1:I+1) = 'r'
ELSE
NAME(I+1:I+1) = 's'
END IF
DO 10 I=JGEL,NGELS
IF (I.NE.IGEL) THEN
NAMEM = RNAMES(I)
IF (NAME.EQ.NAMEM) THEN
NMATE = I
RETURN
END IF
END IF
10 CONTINUE
END
SUBROUTINE LMATES(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,
+IDEV,IGELS,MATES,DIST,RNAMES,NMATES)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER MATES(IDBSIZ),IGELS(IDBSIZ),DIST(IDBSIZ)
CHARACTER*(*) RNAMES(IDBSIZ)
C
C list mates
C
C WRITE(*,*)NMATES
DO 10 I=1,NMATES
J = IGELS(I)
K = MATES(I)
IF(DIST(I).GT.0) THEN
WRITE(IDEV,1000)J,RNAMES(J),RELPG(J),LNGTHG(J),DIST(I)
WRITE(IDEV,1000)K,RNAMES(K),RELPG(K),LNGTHG(K)
1000 FORMAT(' ',I6,' ',A,' ',3I6)
END IF
10 CONTINUE
DO 20 I=1,NMATES
J = IGELS(I)
K = MATES(I)
IF(DIST(I).LT.0) THEN
WRITE(IDEV,1000)J,RNAMES(J),RELPG(J),LNGTHG(J),DIST(I)
WRITE(IDEV,1000)K,RNAMES(K),RELPG(K),LNGTHG(K)
END IF
20 CONTINUE
END
SUBROUTINE CHKREW(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,
+IDEVN,IGELS,MATES,DIST,RNAMES,LLINO,NMATES)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER MATES(IDBSIZ),IGELS(IDBSIZ),DIST(IDBSIZ)
CHARACTER*(*) RNAMES(IDBSIZ)
LOGICAL SAMEC
EXTERNAL NMATE,SAMEC
C
C need to know which ones have already been mated
C
CALL FILLI(IGELS,NGELS,0)
CALL FILLI(MATES,NGELS,0)
CALL GNAMES(IDEVN,RNAMES,NGELS)
IGEL = LLINO
NMATES = 0
10 CONTINUE
MATE = NMATE(IGEL,NGELS,RNAMES,1)
IF (MATE.NE.0) THEN
NMATES = NMATES + 1
IGELS(NMATES) = IGEL
MATES(NMATES) = MATE
C WRITE(*,*)IGELS(NMATES),MATES(NMATES)
C
C we have a pair igel and mate. deal separately with cases of 1 or 2 contigs
C
IF (SAMEC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,NCONTS,IGEL,MATE))
+ THEN
C
C same contig
C
DIST(NMATES) = RELPG(MATE) + ABS(LNGTHG(MATE)) - RELPG(IGEL)
IF(RELPG(MATE).LT.RELPG(IGEL)) THEN
C
C seen it before so skip it
C
NMATES = NMATES - 1
C IGELS(NMATES) = MATE
C MATES(NMATES) = IGEL
END IF
C WRITE(*,*)IGELS(NMATES),MATES(NMATES)
C WRITE(*,*)DIST(NMATES)
ELSE
C
C different contigs
C
DIST(NMATES) = -ABS(LNGTHG(IGELS(NMATES)))
C WRITE(*,*)DIST(NMATES)
END IF
END IF
IF (RNBR(IGEL).NE.0) THEN
IGEL = RNBR(IGEL)
GO TO 10
END IF
END
SUBROUTINE GDEPTH(RELPG,LNGTHG,
+IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),IGELS(NMATES),MATES(NMATES),DIST(NMATES)
INTEGER LNGTHG(IDBSIZ)
INTEGER RREG,DEPTH
C WRITE(*,*)(IGELS(K),MATES(K),DIST(K),K=1,NMATES)
CALL GDPTH(RELPG,
+IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,DEPTH)
IF(NMATES.LT.1) RETURN
CALL PLTCOG(RELPG,LNGTHG,IDBSIZ,IGELS,MATES,DIST,NMATES,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX,LREG,RREG,DEPTH)
END
SUBROUTINE GDPTH(RELPG,
+IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,DEPTH)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),MATES(NMATES),IGELS(NMATES),DIST(NMATES)
INTEGER RREG,DEPTH
EXTERNAL NCDEPM
C LREG = left contig position
C RREG = right '' ''
C
C have nmates reading numbers in igels and mates, their spacings are dist
C dist <0 means they are in different contigs
C the igels numbers are in left to right order
C
I = 1
5 CONTINUE
IF(I.LE.NMATES) THEN
IF((RELPG(IGELS(I))+ABS(DIST(I))-1).LE.LREG) THEN
I = I + 1
GO TO 5
END IF
END IF
DEPTH = 0
10 CONTINUE
IF(I.LT.NMATES) THEN
IF(RELPG(IGELS(I)).LE.RREG) THEN
K = RELPG(IGELS(I)) + ABS(DIST(I))
DEPTH = MAX(NCDEPM(RELPG,IDBSIZ,I,IGELS,NMATES,K),DEPTH)
I = I + 1
GO TO 10
END IF
END IF
C WRITE(*,*)'DEPTH',DEPTH
END
SUBROUTINE PLTCOG(RELPG,LNGTHG,IDBSIZ,IGELS,MATES,DIST,NMATES,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX,LREG,RREG,DEPTH)
INTEGER DEPTH
INTEGER RELPG(IDBSIZ),IGELS(NMATES),MATES(NMATES),DIST(NMATES)
INTEGER LNGTHG(IDBSIZ)
INTEGER RREG
C have window size margt starting at margb
C depths depthp, depthm
CALL VECTOM
CALL FRAME(MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
CALL PLTCG(RELPG,LNGTHG,
+IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX,DEPTH)
CALL VT100M
END
SUBROUTINE PLTCG(RELPG,LNGTHG,
+IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX,DEPTH)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),IGELS(NMATES),MATES(NMATES),DIST(NMATES)
INTEGER LNGTHG(IDBSIZ)
INTEGER RREG,DEPTH
CHARACTER SYM
LOGICAL MATEY
EXTERNAL MATEY
YINC = REAL(ISYMAX) / (DEPTH + 1)
XMIN = LREG
XMAX = RREG
YMAX = ISYMAX
YMIN = 0.
XSLOPE = REAL(MARGR - MARGL)/100.
YSLOPE = YINC/10.
C WRITE(*,*)XMIN,XMAX
I = 1
5 CONTINUE
IF(I.LE.NMATES) THEN
IF((RELPG(IGELS(I))+ABS(DIST(I))-1).LT.LREG) THEN
I = I + 1
GO TO 5
END IF
END IF
N = 0
10 CONTINUE
IF(I.LE.NMATES) THEN
IF(RELPG(IGELS(I)).LE.RREG) THEN
XF = MAX(RELPG(IGELS(I)),LREG)
XT = MIN(ABS(DIST(I))+RELPG(IGELS(I))-1,RREG)
N = N + 1
IF(N.GT.DEPTH) N = 1
YF = N * YINC
C WRITE(*,*)I,IGELS(I),MATES(I),DIST(I)
C WRITE(*,*)RELPG(IGELS(I)),LNGTHG(IGELS(I))
C WRITE(*,*)RELPG(MATES(I)),LNGTHG(MATES(I))
C WRITE(*,*)I,XF,XT
CALL LINE(XT,XF,YF,YF,XMAX,XMIN,YMAX,YMIN,
+ MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
IF (.NOT.(MATEY(IGELS(I),MATES(I),
+ RELPG,LNGTHG,IDBSIZ)).AND.(DIST(I).GT.0)) THEN
XF1 = XF + (XT-XF)/2.
YT1 = YF - YSLOPE
YT2 = YF + YSLOPE
CALL LINE(XF1,XF1,YT1,YT2,XMAX,XMIN,YMAX,YMIN,
+ MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
END IF
IF (LNGTHG(IGELS(I)).GT.0) THEN
XT = RELPG(IGELS(I))+LNGTHG(IGELS(I))
CALL RARROW(XT,YF,XSLOPE,YSLOPE,XMAX,XMIN,YMAX,YMIN,
+ MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
ELSE
XT = MAX(RELPG(IGELS(I)),LREG)
CALL LARROW(XT,YF,XSLOPE,YSLOPE,XMAX,XMIN,YMAX,YMIN,
+ MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
END IF
IF (DIST(I).GT.0) THEN
IF (LNGTHG(MATES(I)).GT.0) THEN
XT = RELPG(MATES(I))+LNGTHG(MATES(I))
CALL RARROW(XT,YF,XSLOPE,YSLOPE,XMAX,XMIN,YMAX,YMIN,
+ MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
ELSE
XT = MIN(RELPG(MATES(I)),RREG)
CALL LARROW(XT,YF,XSLOPE,YSLOPE,XMAX,XMIN,YMAX,YMIN,
+ MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
END IF
ELSE
SYM = '*'
CALL TEXT(XT,YF,SYM,1,ISIZE,XMAX,XMIN,YMAX,YMIN,
+ MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
END IF
I = I + 1
GO TO 10
END IF
END IF
END
SUBROUTINE LARROW(XT,YF,XSLOPE,YSLOPE,XMAX,XMIN,YMAX,YMIN,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
XF1 = XT + XSLOPE
YT1 = YF + YSLOPE
XF2 = XT + XSLOPE
YT2 = YF - YSLOPE
CALL LINE(XT,XF1,YF,YT1,XMAX,XMIN,YMAX,YMIN,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
CALL LINE(XT,XF2,YF,YT2,XMAX,XMIN,YMAX,YMIN,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
END
SUBROUTINE RARROW(XT,YF,XSLOPE,YSLOPE,XMAX,XMIN,YMAX,YMIN,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
XF1 = XT - XSLOPE
YT1 = YF + YSLOPE
XF2 = XT - XSLOPE
YT2 = YF - YSLOPE
CALL LINE(XT,XF1,YF,YT1,XMAX,XMIN,YMAX,YMIN,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
CALL LINE(XT,XF2,YF,YT2,XMAX,XMIN,YMAX,YMIN,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX)
END
LOGICAL FUNCTION MATEY(IGEL,MATE,RELPG,LNGTHG,NGELS)
INTEGER RELPG(NGELS),LNGTHG(NGELS)
MATEY = .FALSE.
IF (RELPG(IGEL).LT.RELPG(MATE)) THEN
IF ((LNGTHG(IGEL).GT.0).AND.(LNGTHG(MATE).LT.0)) MATEY = .TRUE.
ELSE
IF ((LNGTHG(MATE).GT.0).AND.(LNGTHG(IGEL).LT.0)) MATEY = .TRUE.
END IF
END
INTEGER FUNCTION NCDEPM(RELPG,IDBSIZ,IGEL,
+IGELS,NMATES,RREG)
INTEGER RELPG(IDBSIZ)
INTEGER IGELS(NMATES)
INTEGER RREG
NCDEPM = 0
N = 0
I = IGEL
10 CONTINUE
IF(I.LE.NMATES) THEN
IF(RELPG(IGELS(I)).LE.RREG) THEN
N = N + 1
I = I + 1
GO TO 10
END IF
END IF
NCDEPM = N
END
SUBROUTINE XHGAP(RELPG,LNGTHG,LNBR,RNBR,
+IDBSIZ,NCONTS,LLINOI,LINCNI,LREG,RREG,
+WINDOW,GWIND,LENCON,DEPTHP,DEPTHM,
+MARGL,MARGR,MARGB,MARGT,MAXOPT,ISXMAX,ISYMAX,KBIN,IDEV,
+KBOUT,GEL,GEL2,IDEV2,IDEV3,LINLEN,PERCD,MAXGEL,IDM,
+SEQ1,IDIM1,NGELS,TEMP3,CHRSIZ,MAXGL2,LINOU1,LINOU2,
+NOPT1,NOPT2,NOPT3,NOPT4,
+IHELPS,IHELPE,HELPF,IDEVH,MXGOOD,RNAMES,IGELS,MATES,DIST)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),WINDOW,CHRSIZ,GWIND
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER MARGB(MAXOPT),MARGT(MAXOPT)
INTEGER RREG,DEPTHP,DEPTHM,STRAND,CHNRP1,HQN
INTEGER TEMP3(2,CHRSIZ,MAXGL2)
CHARACTER GEL(MAXGEL),GEL2(MAXGEL)
CHARACTER TERM,TUPPER,NAMARC*16,HELPF*(*)
CHARACTER SEQ1(IDIM1),LINOU1(MAXGEL),LINOU2(MAXGEL)
CHARACTER*(*) RNAMES(IDBSIZ)
INTEGER MATES(IDBSIZ),IGELS(IDBSIZ),DIST(IDBSIZ),DEPTHR
EXTERNAL NOPWIN,CWORLD,TUPPER,CHNRP1,HQN
C nopt1 = single contig
C nopt2 = all contigs
C nopt3 = scan
C nopt4 = plot templates with pairs of reads
CALL CHKREW(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,NGELS,
+IDEV3,IGELS,MATES,DIST,RNAMES,LLINOI,NMATES)
10 CONTINUE
LLINO = LLINOI
LINCON = LINCNI
LOCLR = 0
LOCRR = 0
CALL BPAUSE(KBIN,KBOUT,IOK)
CALL CLEARV
CALL XHAIRR(ISXMAX,ISYMAX,IX,IY,TERM,DBTDUX,DBTDUY)
CALL VT100M
INFLAG = HQN(TERM)
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
GO TO 10
END IF
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.3) RETURN
NOPT = NOPWIN(IY,MARGB,MARGT,MAXOPT)
C WRITE(*,*)NOPT
TERM = TUPPER(TERM)
IF(NOPT.EQ.0) RETURN
IF(NOPT.EQ.NOPT3) THEN
IF(TERM.EQ.'S') THEN
XMIN = LREG
XMAX = RREG
X = CWORLD(IX,MARGL,MARGR,XMIN,XMAX)
LOCLR = MAX(LREG,NINT(X)-WINDOW)
LOCRR = MIN(RREG,NINT(X)+WINDOW-1)
IF(LOCLR.NE.0) THEN
CALL DSPLAY(RELPG,LNGTHG,LNBR,RNBR,
+ GEL,LLINO,LINCON,LOCLR,LOCRR,GEL2,I1,I2,0,I,
+ IDBSIZ,IDEV,KBOUT,
+ IDEV2,IDEV3,LINLEN,PERCD,MAXGEL,IDM)
GO TO 10
END IF
END IF
IF((TERM.EQ.'N').OR.(TERM.EQ.'Z').OR.(TERM.EQ.'I')) GO TO 10
END IF
IF(NOPT.EQ.NOPT1) THEN
STRAND = 1
CALL FDPTH(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,LENCON,STRAND,DEPTHP)
IF(DEPTHP.LT.0) RETURN
STRAND = -1
CALL FDPTH(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,LENCON,STRAND,DEPTHM)
IF(DEPTHM.LT.0) RETURN
YMAX = ISYMAX
YMIN = 0.
XMIN = LREG
XMAX = RREG
RINC = ISYMAX / (DEPTHP + DEPTHM + 2)
RMID =(DEPTHM+1) * RINC
X = CWORLD(IX,MARGL,MARGR,XMIN,XMAX)
Y = CWORLD(IY,MARGB(NOPT),MARGT(NOPT),YMIN,YMAX)
C WRITE(*,*)X,Y,IX,IY
IF(TERM.EQ.'I') THEN
STRAND = 1
YINC = RINC * STRAND
CALL IPLTC(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,STRAND,
+ MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),
+ ISXMAX,ISYMAX,RMID,YINC,DEPTHP,X,Y,
+ KBOUT,IGEL,ICLOSE)
IF(ICLOSE.EQ.1) THEN
STRAND = -1
YINC = RINC * STRAND
CALL IPLTC(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,STRAND,
+ MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),
+ ISXMAX,ISYMAX,RMID,YINC,DEPTHM,X,Y,
+ KBOUT,IGEL,ICLOSE)
END IF
IF(ICLOSE.EQ.1) GO TO 10
CALL READN(IDEV3,IGEL,NAMARC)
WRITE(IDEV,1006)NAMARC,IGEL,RELPG(IGEL),LNGTHG(IGEL)
1006 FORMAT
+ ( ' Name ',A,' Number ',I6,' Rel. Posn. ',I7,' Length ',I5)
GO TO 10
END IF
IF(TERM.EQ.'Z') THEN
STRAND = 1
YINC = RINC * STRAND
CALL IPLTC(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,STRAND,
+ MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),
+ ISXMAX,ISYMAX,RMID,YINC,DEPTHP,X,Y,
+ KBOUT,IGEL,ICLOSE)
IF(ICLOSE.EQ.1) THEN
STRAND = -1
YINC = RINC * STRAND
CALL IPLTC(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,STRAND,
+ MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),
+ ISXMAX,ISYMAX,RMID,YINC,DEPTHM,X,Y,
+ KBOUT,IGEL,ICLOSE)
END IF
IF(IGEL.EQ.0) GO TO 10
CALL CLEARG
CALL PLC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,LINCON,IGEL,
+ NCONTS,MARGL,MARGR,MARGB(NOPT2),MARGT(NOPT2),ISXMAX,ISYMAX)
LREG = MAX(1,RELPG(IGEL)-GWIND)
RREG = MIN(RELPG(LINCON),RELPG(IGEL)+GWIND)
LLINO = LNBR(LINCON)
LLINOI = LLINO
LINCNI = LINCON
LENCON = RREG - LREG + 1
CALL FDEPTH(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,LENCON,
+ MARGL,MARGR,MARGB(NOPT1),MARGT(NOPT1),ISXMAX,ISYMAX)
GO TO 10
END IF
IF(TERM.EQ.'S') THEN
LOCLR = MAX(LREG,NINT(X)-WINDOW)
LOCRR = MIN(RREG,NINT(X)+WINDOW-1)
IF(LOCLR.NE.0) THEN
CALL DSPLAY(RELPG,LNGTHG,LNBR,RNBR,
+ GEL,LLINO,LINCON,LOCLR,LOCRR,GEL2,I1,I2,0,I,
+ IDBSIZ,IDEV,KBOUT,
+ IDEV2,IDEV3,LINLEN,PERCD,MAXGEL,IDM)
GO TO 10
END IF
END IF
IF(TERM.EQ.'N') THEN
LOCLR = MAX(LREG,NINT(X)-WINDOW)
LOCRR = MIN(RREG,NINT(X)+WINDOW-1)
IGEL = CHNRP1(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,
+ LLINO,LREG)
IF(LOCLR.NE.0) THEN
CALL LSTCON(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,IGEL,
+ LOCRR,IDEV,IDEV3,NAMARC)
END IF
GO TO 10
END IF
IF(TERM.EQ.'Q') THEN
CALL DBSCNP(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,SEQ1,
+ IDIM1,GEL,IDBSIZ,TEMP3,2,CHRSIZ,MAXGL2,IDEV2,LLINO,
+ PERCD,MAXGEL,LINOU1,LINOU2,LREG,RREG,
+ MARGL,MARGR,MARGB(NOPT3),MARGT(NOPT3),ISXMAX,ISYMAX,
+ MXGOOD)
GO TO 10
END IF
END IF
IF(NOPT.EQ.NOPT2) THEN
CALL IDPLC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,
+ NCONTS,IX,IY,MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),
+ ISXMAX,ISYMAX,DBTDUX,DBTDUY,
+ LINCON,IGEL,IS)
IF(IGEL.EQ.0) RETURN
IF(TERM.EQ.'Z') THEN
CALL CLEARG
CALL PLC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,LINCON,IGEL,
+ NCONTS,MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX)
LREG = 1
RREG = RELPG(LINCON)
LLINO = LNBR(LINCON)
LLINOI = LLINO
LINCNI = LINCON
LENCON = RREG - LREG + 1
CALL FDEPTH(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,LENCON,
+ MARGL,MARGR,MARGB(NOPT1),MARGT(NOPT1),ISXMAX,ISYMAX)
GO TO 10
END IF
IF(TERM.EQ.'Q') THEN
CALL CLEARG
CALL PLC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,LINCON,IGEL,
+ NCONTS,MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX)
LREG = 1
RREG = RELPG(LINCON)
LLINO = LNBR(LINCON)
LLINOI = LLINO
LINCNI = LINCON
LENCON = RREG - LREG + 1
CALL FDEPTH(RELPG,LNGTHG,LNBR,RNBR,
+ IDBSIZ,LLINO,LREG,RREG,LENCON,
+ MARGL,MARGR,MARGB(NOPT1),MARGT(NOPT1),ISXMAX,ISYMAX)
CALL DBSCNP(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,SEQ1,
+ IDIM1,GEL,IDBSIZ,TEMP3,2,CHRSIZ,MAXGL2,IDEV2,LLINO,
+ PERCD,MAXGEL,LINOU1,LINOU2,LREG,RREG,
+ MARGL,MARGR,MARGB(NOPT3),MARGT(NOPT3),ISXMAX,ISYMAX,
+ MXGOOD)
GO TO 10
END IF
IF(TERM.EQ.'I') THEN
CALL READN(IDEV3,IGEL,NAMARC)
WRITE(IDEV,1006)NAMARC,IGEL,RELPG(IGEL),LNGTHG(IGEL)
GO TO 10
END IF
IF(TERM.EQ.'S') THEN
LOCLR = MAX(1,IS-WINDOW)
LOCRR = MIN(RELPG(LINCON),IS+WINDOW-1)
LLINO = LNBR(LINCON)
IF(LOCLR.NE.0) THEN
CALL DSPLAY(RELPG,LNGTHG,LNBR,RNBR,
+ GEL,LLINO,LINCON,LOCLR,LOCRR,GEL2,I1,I2,0,I,
+ IDBSIZ,IDEV,KBOUT,
+ IDEV2,IDEV3,LINLEN,PERCD,MAXGEL,IDM)
END IF
GO TO 10
END IF
IF(TERM.EQ.'N') THEN
LOCLR = MAX(1,IS-WINDOW)
LOCRR = MIN(RELPG(LINCON),IS+WINDOW-1)
LLINO = LNBR(LINCON)
IF(LOCLR.NE.0) THEN
CALL LSTCON(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,IGEL,
+ LOCRR,IDEV,IDEV3,NAMARC)
END IF
GO TO 10
END IF
END IF
IF(NOPT.EQ.NOPT4) THEN
CALL GDPTH(RELPG,
+ IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,DEPTHR)
C + MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX)
IF(DEPTHR.LT.0) RETURN
YMAX = ISYMAX
YMIN = 0.
XMIN = LREG
XMAX = RREG
X = CWORLD(IX,MARGL,MARGR,XMIN,XMAX)
Y = CWORLD(IY,MARGB(NOPT),MARGT(NOPT),YMIN,YMAX)
C WRITE(*,*)X,Y,IX,IY
IF(TERM.EQ.'I') THEN
CALL IPLTCG(RELPG,LNGTHG,
+ IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,
+ MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX,DEPTHR,X,Y,
+ IGEL,ICLOSE)
IF(ICLOSE.EQ.1) GO TO 10
C CALL READN(IDEV3,IGEL,NAMARC)
J = IGELS(IGEL)
WRITE(IDEV,1007)RNAMES(J),J,RELPG(J),LNGTHG(J)
J = MATES(IGEL)
WRITE(IDEV,1007)RNAMES(J),J,RELPG(J),LNGTHG(J)
1007 FORMAT(' 'A,3I6)
C WRITE(IDEV,1006)NAMARC,IGEL,RELPG(IGEL),LNGTHG(IGEL)
GO TO 10
END IF
END IF
END
SUBROUTINE IPLTCG(RELPG,LNGTHG,
+IDBSIZ,LREG,RREG,IGELS,MATES,DIST,NMATES,
+MARGL,MARGR,MARGB,MARGT,ISXMAX,ISYMAX,DEPTH,X,Y,IGEL,IOK)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),IGELS(NMATES),MATES(NMATES),DIST(NMATES)
INTEGER LNGTHG(IDBSIZ)
INTEGER RREG,DEPTH
LOGICAL MATEY
EXTERNAL MATEY
YINC = REAL(ISYMAX) / (DEPTH + 1)
YINCO2 = YINC/2.
XMIN = LREG
XMAX = RREG
YMAX = ISYMAX
YMIN = 0.
C WRITE(*,*)X,Y
C WRITE(*,*)XMIN,XMAX,YMIN,YMAX,YINC
I = 1
5 CONTINUE
IF(I.LE.NMATES) THEN
IF((RELPG(IGELS(I))+ABS(DIST(I))-1).LT.LREG) THEN
I = I + 1
GO TO 5
END IF
END IF
N = 0
10 CONTINUE
IF(I.LE.NMATES) THEN
IF(RELPG(IGELS(I)).LE.RREG) THEN
XF = MAX(RELPG(IGELS(I)),LREG)
XT = MIN(ABS(DIST(I))+RELPG(IGELS(I))-1,RREG)
N = N + 1
IF(N.GT.DEPTH) N = 1
YF = N * YINC
C WRITE(*,*)XF,XT,YF
C WRITE(*,*)I,IGELS(I),MATES(I),DIST(I)
C WRITE(*,*)RELPG(IGELS(I)),LNGTHG(IGELS(I))
C WRITE(*,*)RELPG(MATES(I)),LNGTHG(MATES(I))
C WRITE(*,*)I,XF,XT
IF((X.GE.XF).AND.(X.LE.XT)) THEN
IF((Y.GE.YF-YINCO2).AND.(Y.LE.YF+YINCO2)) THEN
IOK = 0
IGEL = I
RETURN
END IF
END IF
I = I + 1
GO TO 10
END IF
END IF
IOK = 1
END
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