287 lines
6.7 KiB
C
287 lines
6.7 KiB
C
/*
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Title: seqIOSCF
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File: seqIOSCF.c
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Purpose: IO of Standard Chromatogram Format sequences
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Last update: Tue Nov 10 1992
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Change log:
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4 Feb 1992, Now draft proposal version 2
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20 Feb 1992, Grab info from comment lines
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19 Aug 1992, If SCF file has clip information, don't clip automatically
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10 Nov 1992 SCF comments now stored in seq data structure
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*/
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/* ---- Imports ---- */
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#include "scf.h" /* SCF structures */
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#include "seq.h" /* IMPORT: Seq, BasesAndTraces, NULLSeq,
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newSeq, freeSeq */
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#include "seqIOEdit.h" /* IMPORT: writeEdSeq,
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readEdSEq */
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#include <ctype.h>
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#include <stdio.h> /* IMPORT: fopen, fclose, fseek, ftell, fgetc,
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EOF */
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#include <stdlib.h>
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#include "mach-io.h"
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/* ---- Internal functions ---- */
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static int read_scf_header(FILE *fp, Header *h)
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{
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int i;
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if (be_read_int_4(fp,&h->magic_number)==False) return (False);
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if (be_read_int_4(fp,&h->samples)==False) return (False);
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if (be_read_int_4(fp,&h->samples_offset)==False) return (False);
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if (be_read_int_4(fp,&h->bases)==False) return (False);
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if (be_read_int_4(fp,&h->bases_left_clip)==False) return (False);
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if (be_read_int_4(fp,&h->bases_right_clip)==False) return (False);
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if (be_read_int_4(fp,&h->bases_offset)==False) return (False);
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if (be_read_int_4(fp,&h->comments_size)==False) return (False);
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if (be_read_int_4(fp,&h->comments_offset)==False) return (False);
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if (fread(&h->version[0],sizeof(h->version),1,fp)!=1) return (False);
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if (be_read_int_4(fp,&h->sample_size)==False) return (False);
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if (be_read_int_4(fp,&h->code_set)==False) return (False);
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for (i=0;i<20;i++)
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if (be_read_int_4(fp,&h->spare[i])==False) return (False);
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return (True);
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}
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static int read_scf_sample1(FILE *fp, Samples1 *s)
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{
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if (be_read_int_1(fp,&s->sample_A)==False) return (False);
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if (be_read_int_1(fp,&s->sample_C)==False) return (False);
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if (be_read_int_1(fp,&s->sample_G)==False) return (False);
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if (be_read_int_1(fp,&s->sample_T)==False) return (False);
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return (True);
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}
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static int read_scf_sample2(FILE *fp, Samples2 *s)
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{
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if (be_read_int_2(fp,&s->sample_A)==False) return (False);
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if (be_read_int_2(fp,&s->sample_C)==False) return (False);
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if (be_read_int_2(fp,&s->sample_G)==False) return (False);
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if (be_read_int_2(fp,&s->sample_T)==False) return (False);
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return (True);
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}
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static int read_scf_base(FILE *fp, Bases *b)
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{
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if (be_read_int_4(fp,&b->peak_index)==False) return (False);
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if (be_read_int_1(fp,&b->prob_A)==False) return (False);
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if (be_read_int_1(fp,&b->prob_C)==False) return (False);
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if (be_read_int_1(fp,&b->prob_G)==False) return (False);
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if (be_read_int_1(fp,&b->prob_T)==False) return (False);
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if (be_read_int_1(fp,(byte *)&b->base)==False) return (False);
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if (be_read_int_1(fp,&b->spare[0])==False) return (False);
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if (be_read_int_1(fp,&b->spare[1])==False) return (False);
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if (be_read_int_1(fp,&b->spare[2])==False) return (False);
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return (True);
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}
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static float parse_version(char version[])
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/*
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*
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*/
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{
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char v[5];
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strncpy(v,version,4);v[4]='\0';
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if (strspn(v,"0123456789. ")!=4) return 0.0;
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return atof(v);
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}
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/* ---- Exports ---- */
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int is_SCF(char *fn)
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/*
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* Check to see if file with name `fn' is in SCF format
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*
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* Returns:
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* 1 - is SCF format
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* 0 - not SCF format
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*/
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{
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FILE *fp;
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uint_4 magic;
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int ok;
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if ( (fp=fopen(fn,"rb")) == NULL) {
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ok = 0;
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} else {
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if ( be_read_int_4(fp, &magic) != 1 ) {
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ok = 0;
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} else {
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ok = (magic==SCF_MAGIC);
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}
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fclose(fp);
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}
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return ok;
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}
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Seq readSeqSCF(char *fn)
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/*
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* Read the SCF format sequence with name `fn' into `seq'.
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* If bottom is True, we read the sequence in in reverse and
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* complemented A NULL result indicates failure.
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*/
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{ Seq seq = NULLSeq;
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FILE *fp;
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Header header;
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int i;
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/* Open for: reading, binary */
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if ((fp = fopen(fn, "rb")) == NULL) return(NULLSeq);
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/* Read header */
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if (fseek(fp, (off_t)0, 0) != 0) {
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fclose(fp);
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return(NULLSeq);
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}
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if (read_scf_header(fp,&header)==False) {
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fclose(fp);
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return(NULLSeq);
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}
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/* Allocate the sequence */
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if ((seq = newSeq(BasesAndTraces, header.samples, header.bases)) == NULLSeq)
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{ fclose(fp);
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return(NULLSeq);
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}
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seq->mode = BasesAndTraces;
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seq->format = SCFFormat;
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seq->dirty = False;
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seq->maxTraceVal = 0;
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seq->NPoints = header.samples;
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seq->NorigBases = header.bases;
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seq->NedBases = header.bases;
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seq->leftCutoff = header.bases_left_clip;
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seq->rightCutoff = header.bases_right_clip;
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seq->bottom = False;
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/* set precision if necessary */
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if (parse_version(header.version)<VERSION) {
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/* old 8-bit format */
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header.sample_size = 1;
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}
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/* read sample points */
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if (fseek(fp, (off_t)(header.samples_offset), 0) != 0) {
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fclose(fp);
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return(NULLSeq);
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}
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for(i=0;i<seq->NPoints;i++) {
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switch ( header.sample_size ) {
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case 2:
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{
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Samples2 sample;
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if (read_scf_sample2(fp,&sample)==False) {
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fclose(fp);
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return(NULLSeq);
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}
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seq->traceA[i] = sample.sample_A;
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seq->traceC[i] = sample.sample_C;
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seq->traceG[i] = sample.sample_G;
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seq->traceT[i] = sample.sample_T;
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break;
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}
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default:
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{
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Samples1 sample;
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if (read_scf_sample1(fp,&sample)==False) {
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fclose(fp);
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return(NULLSeq);
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}
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seq->traceA[i] = sample.sample_A;
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seq->traceC[i] = sample.sample_C;
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seq->traceG[i] = sample.sample_G;
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seq->traceT[i] = sample.sample_T;
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break;
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}
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}
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if (seq->maxTraceVal < seq->traceA[i]) seq->maxTraceVal = seq->traceA[i];
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if (seq->maxTraceVal < seq->traceC[i]) seq->maxTraceVal = seq->traceC[i];
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if (seq->maxTraceVal < seq->traceG[i]) seq->maxTraceVal = seq->traceG[i];
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if (seq->maxTraceVal < seq->traceT[i]) seq->maxTraceVal = seq->traceT[i];
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}
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/* Read bases */
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if (fseek(fp, (off_t)(header.bases_offset), 0) != 0) {
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fclose(fp);
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return(NULLSeq);
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}
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for(i=0;i<seq->NorigBases;i++) {
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Bases base;
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if (read_scf_base(fp,&base)==False) {
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fclose(fp);
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return(NULLSeq);
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}
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seq->base[i] = base.base;
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seq->basePos[i] = base.peak_index;
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}
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/* Read selected comment information */
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{
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char *comments;
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comments = (char *) malloc(header.comments_size+1);
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if (fseek(fp,(off_t)(header.comments_offset), 0) != 0) {
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free(comments);
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fclose(fp);
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return(NULLSeq);
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}
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if (fread(comments,header.comments_size,1,fp)==0) {
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free(comments);
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fclose(fp);
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return(NULLSeq);
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}
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comments[header.comments_size] = '\0';
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seq->info = comments;
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}
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/* Finished with the file */
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fclose(fp);
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return(seq);
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}
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