111 lines
3.4 KiB
C
111 lines
3.4 KiB
C
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/* flags_demo.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 <unistd.h>
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#include <htslib/sam.h>
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/// print_usage - show 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: flags <infile>\n\
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Shows the count of read1 and read2 alignments\n\
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This shows basic reading and alignment flag access\n");
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return;
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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; //input file name
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int c = 0, ret = EXIT_FAILURE;
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int64_t cntread1 = 0, cntread2 = 0; //count
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samFile *infile = NULL; //sam file
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sam_hdr_t *in_samhdr = NULL; //header of file
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bam1_t *bamdata = NULL; //to hold the read data
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if (argc != 2) {
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print_usage(stdout);
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goto end;
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}
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inname = argv[1];
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//initialize
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if (!(bamdata = bam_init1())) {
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printf("Failed to initialize bamdata\n");
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goto end;
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}
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//open input files - r reading
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if (!(infile = sam_open(inname, "r"))) {
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printf("Could not open %s\n", inname);
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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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//read data, check flags and update count
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while ((c = sam_read1(infile, in_samhdr, bamdata)) >= 0) {
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if (bamdata->core.flag & BAM_FREAD1) {
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cntread1++;
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}
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if (bamdata->core.flag & BAM_FREAD2) {
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cntread2++;
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}
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}
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if (c != -1) {
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//error
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printf("Failed to get data\n");
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goto end;
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}
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//else -1 / EOF
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printf("File %s has %"PRIhts_pos" read1 and %"PRIhts_pos" read2 alignments\n", inname, cntread1, cntread2);
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ret = EXIT_SUCCESS;
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end:
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//clean up
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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 (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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