169 lines
6.5 KiB
C
169 lines
6.5 KiB
C
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/* cram.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: cram infile reffile outdir\n\
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Dumps the input file alignments in cram format in given directory\n\
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1.cram has external reference\n\
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2.cram has reference embedded\n\
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3.cram has autogenerated reference\n\
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4.cram has no reference data in it\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, *outdir = NULL, *reffile = NULL;
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char *file1 = NULL, *file2 = NULL, *file3 = NULL, *file4 = NULL, *reffmt1 = NULL, *reffmt2 = NULL;
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int c = 0, ret = EXIT_FAILURE, size1 = 0, size2 = 0, size3 = 0;
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samFile *infile = NULL, *outfile1 = NULL, *outfile2 = NULL, *outfile3 = NULL, *outfile4 = NULL;
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sam_hdr_t *in_samhdr = NULL;
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bam1_t *bamdata = NULL;
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htsFormat fmt1 = {0}, fmt2 = {0}, fmt3 = {0}, fmt4 = {0};
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//cram infile reffile outdir
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if (argc != 4) {
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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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reffile = argv[2];
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outdir = argv[3];
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//allocate space for option string and output file names
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size1 = sizeof(char) * (strlen(reffile) + sizeof("cram,reference=") + 1);
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size2 = sizeof(char) * (strlen(reffile) + sizeof("cram,embed_ref=1,reference=") + 1);
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size3 = sizeof(char) * (strlen(outdir) + sizeof("/1.cram") + 1);
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reffmt1 = malloc(size1); reffmt2 = malloc(size2);
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file1 = malloc(size3); file2 = malloc(size3);
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file3 = malloc(size3); file4 = malloc(size3);
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if (!file1 || !file2 || !file3 || !file4 || !reffmt1 || !reffmt2) {
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printf("Failed to create buffers\n");
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goto end;
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}
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snprintf(reffmt1, size1, "cram,reference=%s", reffile);
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snprintf(reffmt2, size2, "cram,embed_ref=1,reference=%s", reffile);
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snprintf(file1, size3, "%s/1.cram", outdir); snprintf(file2, size3, "%s/2.cram", outdir);
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snprintf(file3, size3, "%s/3.cram", outdir); snprintf(file4, size3, "%s/4.cram", outdir);
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if (hts_parse_format(&fmt1, reffmt1) == -1 || //using external reference - uses the M5/UR tags to get reference data during read
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hts_parse_format(&fmt2, reffmt2) == -1 || //embed the reference internally
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hts_parse_format(&fmt3, "cram,embed_ref=2") == -1 || //embed autogenerated reference
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hts_parse_format(&fmt4, "cram,no_ref=1") == -1) { //no reference data encoding at all
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printf("Failed to set output option\n");
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goto end;
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}
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//bam data storage
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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 file - 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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//open output files - w write as SAM, wb write as BAM, wc as CRAM (equivalent to fmt3)
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outfile1 = sam_open_format(file1, "wc", &fmt1); outfile2 = sam_open_format(file2, "wc", &fmt2);
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outfile3 = sam_open_format(file3, "wc", &fmt3); outfile4 = sam_open_format(file4, "wc", &fmt4);
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if (!outfile1 || !outfile2 || !outfile3 || !outfile4) {
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printf("Could not open output file\n");
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goto end;
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}
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//read header, required to resolve the target names to proper ids
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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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//write header
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if ((sam_hdr_write(outfile1, in_samhdr) == -1) || (sam_hdr_write(outfile2, in_samhdr) == -1) ||
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(sam_hdr_write(outfile3, in_samhdr) == -1) || (sam_hdr_write(outfile4, 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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//check flags and write
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while ((c = sam_read1(infile, in_samhdr, bamdata)) >= 0) {
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if (sam_write1(outfile1, in_samhdr, bamdata) < 0 ||
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sam_write1(outfile2, in_samhdr, bamdata) < 0 ||
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sam_write1(outfile3, in_samhdr, bamdata) < 0 ||
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sam_write1(outfile4, in_samhdr, bamdata) < 0) {
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printf("Failed to write output data\n");
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goto end;
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}
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}
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if (-1 == c) {
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//EOF
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ret = EXIT_SUCCESS;
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}
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else {
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printf("Error in reading data\n");
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}
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end:
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#define IF_OL(X,Y) if((X)) {(Y);} //if one liner
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//cleanup
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IF_OL(in_samhdr, sam_hdr_destroy(in_samhdr));
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IF_OL(infile, sam_close(infile));
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IF_OL(outfile1, sam_close(outfile1));
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IF_OL(outfile2, sam_close(outfile2));
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IF_OL(outfile3, sam_close(outfile3));
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IF_OL(outfile4, sam_close(outfile4));
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IF_OL(file1, free(file1));
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IF_OL(file2, free(file2));
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IF_OL(file3, free(file3));
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IF_OL(file4, free(file4));
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IF_OL(reffmt1, free(reffmt1));
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IF_OL(reffmt2, free(reffmt2));
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IF_OL(fmt1.specific, hts_opt_free(fmt1.specific));
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IF_OL(fmt2.specific, hts_opt_free(fmt2.specific));
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IF_OL(fmt3.specific, hts_opt_free(fmt3.specific));
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IF_OL(fmt4.specific, hts_opt_free(fmt4.specific));
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IF_OL(bamdata, bam_destroy1(bamdata));
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return ret;
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}
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