126 lines
3.8 KiB
C
126 lines
3.8 KiB
C
/* read_refname.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 - 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: read_refname infile minsize\n\
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This shows name of references which has length above the given size\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, *id = NULL;
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int c = 0, ret = EXIT_FAILURE, linecnt = 0, pos = 0;
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samFile *infile = NULL;
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sam_hdr_t *in_samhdr = NULL;
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kstring_t data = KS_INITIALIZE;
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int64_t minsize = 0, size = 0;
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if (argc != 3 && 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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if (argc == 3) {
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minsize = atoll(argv[2]);
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}
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//open input files
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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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linecnt = sam_hdr_count_lines(in_samhdr, "SQ"); //get reference count
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if (linecnt <= 0) {
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if (!linecnt) {
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printf("No reference line present\n");
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}
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else {
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printf("Failed to get reference line count\n");
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}
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goto end;
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}
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//iterate and check each reference's length
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for (pos = 1, c = 0; c < linecnt; ++c) {
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if ((ret = sam_hdr_find_tag_pos(in_samhdr, "SQ", c, "LN", &data) == -2)) {
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printf("Failed to get length\n");
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goto end;
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}
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else if (ret == -1) {
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//length not present, ignore
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continue;
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}
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//else have length
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size = atoll(data.s);
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if (size < minsize) {
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//not required
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continue;
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}
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if (!(id = sam_hdr_line_name(in_samhdr, "SQ", c))) { //sam_hdr_find_tag_pos(in_samhdr, "SQ", c, "SN", &data) can also do the same!
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printf("Failed to get id for reference data\n");
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goto end;
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}
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printf("%d,%s,%s\n", pos, id, data.s);
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pos++;
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}
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ret = EXIT_SUCCESS;
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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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ks_free(&data);
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return ret;
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}
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