73 lines
2.3 KiB
C
73 lines
2.3 KiB
C
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/* index_fasta.c -- showcases the htslib api usage
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Copyright (C) 2024 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 <time.h>
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#include <htslib/sam.h>
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#include <htslib/faidx.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: index_fasta <file>\n\
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Indexes a fasta/fastq file and saves along with source.\n");
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return;
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}
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/// main - indexes fasta/fastq file
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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 *filename = NULL; //file name
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int ret = EXIT_FAILURE;
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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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filename = argv[1];
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// index the file
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if (fai_build3(filename, NULL, NULL) == -1) {
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printf("Indexing failed with %d\n", errno);
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goto end;
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}
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//this creates an .fai file. If the file is bgzipped, a .gzi file will be created along with .fai
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ret = EXIT_SUCCESS;
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end:
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//clean up
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return ret;
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}
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