231 lines
7.9 KiB
C
231 lines
7.9 KiB
C
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/* mod_bam.c -- showcases the htslib api usage
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Copyright (C) 2023 Genome Research Ltd.
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Author: Vasudeva Sarma <vasudeva.sarma@sanger.ac.uk>
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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DEALINGS IN THE SOFTWARE
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*/
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/* The purpose of this code is to demonstrate the library apis and need proper error handling and optimisation */
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#include <getopt.h>
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#include <strings.h>
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#include <unistd.h>
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#include <htslib/sam.h>
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/// print_usage - print the usage
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/** @param fp pointer to the file / terminal to which usage to be dumped
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returns nothing
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*/
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static void print_usage(FILE *fp)
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{
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fprintf(fp, "Usage: mod_bam infile QNAME fieldpos newval\n\
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Modifies the alignment data field\n\
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fieldpos - 1 QNAME 2 FLAG 3 RNAME 4 POS 5 MAPQ 6 CIGAR 7 RNEXT 8 PNEXT 9 TLEN 10 SEQ 11 QUAL\n");
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}
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/// main_demo - start of the demo
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/** @param argc - count of arguments
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* @param argv - pointer to array of arguments
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returns 1 on failure 0 on success
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*/
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int main(int argc, char *argv[])
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{
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const char *inname = NULL, *qname = NULL;
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char *val = NULL;
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int c = 0, ret = EXIT_FAILURE, field = 0;
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sam_hdr_t *in_samhdr = NULL;
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samFile *infile = NULL, *outfile = NULL;
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int ret_r = 0, i = 0;
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bam1_t *bamdata = NULL;
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//mod_bam infile QNAME fieldpos newval
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if (argc != 5) {
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print_usage(stderr);
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goto end;
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}
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inname = argv[1];
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qname = argv[2];
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//1 QNAME 2 FLAG 3 RNAME 4 POS 5 MAPQ 6 CIGAR 7 RNEXT 8 PNEXT 9 TLEN 10 SEQ 11 QUAL
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field = atoi(argv[3]);
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val = argv[4];
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if (!(bamdata = bam_init1())) {
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printf("Failed to allocate data memory!\n");
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goto end;
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}
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//open input file
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if (!(infile = sam_open(inname, "r")) || !(outfile = sam_open("-", "w"))) {
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printf("Could not open input/output\n");
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goto end;
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}
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//read header
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if (!(in_samhdr = sam_hdr_read(infile))) {
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printf("Failed to read header from file!\n");
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goto end;
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}
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if (sam_hdr_write(outfile, in_samhdr) == -1) {
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printf("Failed to write header\n");
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goto end;
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}
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while ((ret_r = sam_read1(infile, in_samhdr, bamdata)) >= 0)
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{
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//QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL [TAG:TYPE:VALUE]…
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ret = 0;
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if (!strcasecmp(qname, bam_get_qname(bamdata))) {
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//the required one
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switch(field) {
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case 1:// QNAME
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ret = bam_set_qname(bamdata, val);
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break;
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case 2:// FLAG
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bamdata->core.flag = atol(val) & 0xFFFF;
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break;
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case 3:// RNAME
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case 7:// RNEXT
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if ((ret = sam_hdr_name2tid(in_samhdr, val)) < 0) {
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printf("Invalid reference name\n");
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ret = -1;
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break;
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}
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if (field == 3) {
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//reference
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bamdata->core.tid = ret;
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}
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else {
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//mate reference
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bamdata->core.mtid = ret;
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}
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break;
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case 4:// POS
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bamdata->core.pos = atoll(val);
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break;
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case 5:// MAPQ
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bamdata->core.qual = atoi(val) & 0x0FF;
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break;
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case 6:// CIGAR
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{
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uint32_t *cigar = NULL;
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size_t size = 0;
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ssize_t ncigar = 0;
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bam1_t *newbam = bam_init1();
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if (!newbam) {
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printf("Failed to create new bam data\n");
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ret = -1;
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break;
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}
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//get cigar array and set all data in new bam record
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if ((ncigar = sam_parse_cigar(val, NULL, &cigar, &size)) < 0) {
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printf("Failed to parse cigar\n");
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ret = -1;
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break;
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}
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if (bam_set1(newbam, bamdata->core.l_qname, bam_get_qname(bamdata), bamdata->core.flag, bamdata->core.tid, bamdata->core.pos, bamdata->core.qual,
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ncigar, cigar, bamdata->core.mtid, bamdata->core.mpos, bamdata->core.isize, bamdata->core.l_qseq, (const char*)bam_get_seq(bamdata), (const char*)bam_get_qual(bamdata), bam_get_l_aux(bamdata)) < 0) {
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printf("Failed to set bamdata\n");
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ret = -1;
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break;
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}
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//correct sequence data as input is expected in ascii format and not as compressed inside bam!
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memcpy(bam_get_seq(newbam), bam_get_seq(bamdata), (bamdata->core.l_qseq + 1) / 2);
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//copy the aux data
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memcpy(bam_get_aux(newbam), bam_get_aux(bamdata), bam_get_l_aux(bamdata));
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bam_destroy1(bamdata);
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bamdata = newbam;
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}
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break;
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case 8:// PNEXT
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bamdata->core.mpos = atoll(val);
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break;
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case 9:// TLEN
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bamdata->core.isize = atoll(val);
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break;
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case 10:// SEQ
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i = strlen(val);
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if (bamdata->core.l_qseq != i) {
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printf("SEQ length different\n");
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ret = -1;
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//as it is different, have to update quality data and cigar data as well and more info is required for it, which is not handled in this sample
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//accessing raw memory and moving is one option; creating and using new bam1_t object is another option.
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break;
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}
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for( c = 0; c < i; ++c) {
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bam_set_seqi(bam_get_seq(bamdata), c, seq_nt16_table[(unsigned char)val[c]]);
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}
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break;
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case 11:// QUAL
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i = strlen(val);
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if (i != bamdata->core.l_qseq) {
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printf("Qual length different than sequence\n");
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ret = -1;
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break;
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}
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for (c = 0; c < i; ++c) {
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val[c] -= 33; //phred score from ascii value
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}
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memcpy(bam_get_qual(bamdata), val, i);
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break;
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default:
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printf("Invalid input\n");
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goto end;
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break;
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}
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if (ret < 0) {
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printf("Failed to set new data\n");
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ret = EXIT_FAILURE;
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goto end;
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}
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}
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if (sam_write1(outfile, in_samhdr, bamdata) < 0) {
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printf("Failed to write bam data\n");
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ret = EXIT_FAILURE;
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goto end;
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}
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}
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if (ret_r == -1 || ret != EXIT_FAILURE) {
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// no error!
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ret = EXIT_SUCCESS;
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}
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else {
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printf("Failed to read data\n");
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}
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end:
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//cleanup
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if (in_samhdr) {
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sam_hdr_destroy(in_samhdr);
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}
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if (infile) {
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sam_close(infile);
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}
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if (outfile) {
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sam_close(outfile);
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}
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if (bamdata) {
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bam_destroy1(bamdata);
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}
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return ret;
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}
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