malacology/staden-lg
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base: malacology:5e8a7a252003d66a9ee91d5cff44d788d24a20c8
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malacology:dev
malacology:main
malacology:12.1.1
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compare: malacology:3b42fb10b0ff625873adcfc046f8d25b8bb68e2e
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malacology:dev
malacology:main
malacology:12.1.1

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5e8a7a2520 ... 3b42fb10b0

52 changed files with 11 additions and 33 deletions
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shell/bap
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@ -1,2 +0,0 @@
#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/bap

2
shell/dap
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@ -1,2 +0,0 @@
#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/dap

2
shell/mep
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@ -1,2 +0,0 @@
#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/mep

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shell/nipf
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@ -1,2 +0,0 @@
#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPNIP=/usr/share/staden-lg/help/dap_help NIPHELP=/usr/share/staden-lg/help/NIP.HLP NIPHPNT=/usr/share/staden-lg/help/NIP.PNT NIPMARG=/usr/share/staden-lg/help/NIP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/nipf

2
shell/sap
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#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/sap

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shell/xbap
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#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xbap

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shell/xdap
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#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xdap

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shell/xmep
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#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xmep

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shell/xsap
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#!/bin/bash
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xsap

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src/abi/makefile-alpha
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@ -5,8 +5,7 @@
# #
# Programs made by this makefile # Programs made by this makefile
# #
PROGS = getABISampleName 2rs PROGS = getABISampleName
all: $(PROGS)
# #
# Where the wild things are # Where the wild things are
@ -27,8 +26,6 @@ LDFLAGS = -g
getABISampleName: getABISampleName.o getABISampleName: getABISampleName.o
$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o $(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
2rs: 2rs.o
$(LD) $(LDFLAGS) -o 2rs 2rs.o
# #
# Special dependencies # Special dependencies

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src/cop/makefile-alpha
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@ -6,7 +6,7 @@
# Programs made by this makefile # Programs made by this makefile
# #
PROGS = cop cop-bap PROGS = cop cop-bap
all: $(PROGS)
# #
# Where the wild things are # Where the wild things are
# #

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src/getMCH/makefile-alpha
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@ -23,7 +23,7 @@
# Programs made by this makefile # Programs made by this makefile
# #
PROGS = getMCH trace2seq PROGS = getMCH trace2seq
all: $(PROGS)
# #
# Where the wild things are # Where the wild things are
# #

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src/indexseqlibs/excludewords.c
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@ -13,7 +13,7 @@ static FILE *out;
static int line_comp(char *ex, char *in, int l) static int line_comp(char *ex, char *in, int l)
/* /*
** Compare exclude line with cinline ** Compare exclude line with inline
*/ */
{ {
return strncmp(ex,in+11,l); return strncmp(ex,in+11,l);
@ -28,13 +28,13 @@ static void process()
*/ */
{ {
char exline[MAXLINE]; char exline[MAXLINE];
char cinline[MAXLINE]; char inline[MAXLINE];
char *exok, *inok; char *exok, *inok;
int compare; int compare;
exok = fgets(exline,MAXLINE,ex); exok = fgets(exline,MAXLINE,ex);
inok = fgets(cinline,MAXLINE,in); inok = fgets(inline,MAXLINE,in);
while (exok && inok) { while (exok && inok) {
@ -43,15 +43,15 @@ static void process()
if (compare < 0) if (compare < 0)
exok = fgets(exline,MAXLINE,ex); exok = fgets(exline,MAXLINE,ex);
else if (compare > 0) { else if (compare > 0) {
fprintf(out,"%s",cinline); fprintf(out,"%s",inline);
inok = fgets(cinline,MAXLINE,in); inok = fgets(inline,MAXLINE,in);
} else } else
inok = fgets(cinline,MAXLINE,in); inok = fgets(inline,MAXLINE,in);
} }
while (inok = fgets(cinline,MAXLINE,in)) while (inok = fgets(inline,MAXLINE,in))
fprintf(out,"%s",cinline); fprintf(out,"%s",inline);
} }

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src/indexseqlibs/makefile-alpha
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@ -2,7 +2,6 @@
# indexseqlibs - Alpha version # indexseqlibs - Alpha version
# #
all: $(PROGS)
# #
# Programs need making # Programs need making