148 lines
4.1 KiB
C
148 lines
4.1 KiB
C
/* mod_aux_ba.c -- showcases the htslib api usage
|
|
|
|
Copyright (C) 2023 Genome Research Ltd.
|
|
|
|
Author: Vasudeva Sarma <vasudeva.sarma@sanger.ac.uk>
|
|
|
|
Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
of this software and associated documentation files (the "Software"), to deal
|
|
in the Software without restriction, including without limitation the rights
|
|
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
copies of the Software, and to permit persons to whom the Software is
|
|
furnished to do so, subject to the following conditions:
|
|
|
|
The above copyright notice and this permission notice shall be included in
|
|
all copies or substantial portions of the Software.
|
|
|
|
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
|
|
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
|
|
DEALINGS IN THE SOFTWARE
|
|
|
|
*/
|
|
|
|
/* The purpose of this code is to demonstrate the library apis and need proper error handling and optimisation */
|
|
|
|
#include <getopt.h>
|
|
#include <unistd.h>
|
|
#include <htslib/sam.h>
|
|
|
|
/// print_usage - print the usage
|
|
/** @param fp pointer to the file / terminal to which usage to be dumped
|
|
returns nothing
|
|
*/
|
|
static void print_usage(FILE *fp)
|
|
{
|
|
fprintf(fp, "Usage: mod_aux_ba infile\n\
|
|
Updates the count of bases as an aux array on all alignments\n\
|
|
BA:B:I,count of ACTGN\n");
|
|
}
|
|
|
|
/// main_demo - start of the demo
|
|
/** @param argc - count of arguments
|
|
* @param argv - pointer to array of arguments
|
|
returns 1 on failure 0 on success
|
|
*/
|
|
int main(int argc, char *argv[])
|
|
{
|
|
const char *inname = NULL;
|
|
int i = 0, ret = EXIT_FAILURE, ret_r = 0;
|
|
uint32_t cnt[5] = {0}; //A C G T N
|
|
sam_hdr_t *in_samhdr = NULL;
|
|
samFile *infile = NULL, *outfile = NULL;
|
|
bam1_t *bamdata = NULL;
|
|
|
|
//mod_aux infile
|
|
if (argc != 2) {
|
|
print_usage(stderr);
|
|
goto end;
|
|
}
|
|
inname = argv[1];
|
|
|
|
if (!(bamdata = bam_init1())) {
|
|
printf("Failed to allocate data memory!\n");
|
|
goto end;
|
|
}
|
|
|
|
//open input file
|
|
if (!(infile = sam_open(inname, "r"))) {
|
|
printf("Could not open %s\n", inname);
|
|
goto end;
|
|
}
|
|
|
|
//open output file
|
|
if (!(outfile = sam_open("-", "w"))) {
|
|
printf("Could not open std output\n");
|
|
goto end;
|
|
}
|
|
|
|
if (!(in_samhdr = sam_hdr_read(infile))) {
|
|
printf("Failed to read header from file!\n");
|
|
goto end;
|
|
}
|
|
|
|
if (sam_hdr_write(outfile, in_samhdr) == -1) {
|
|
printf("Failed to write header\n");
|
|
goto end;
|
|
}
|
|
|
|
while ((ret_r = sam_read1(infile, in_samhdr, bamdata)) >= 0) {
|
|
errno = 0;
|
|
memset(cnt, 0, sizeof(cnt));
|
|
for (i = 0; i < bamdata->core.l_qseq; ++i) {
|
|
switch (seq_nt16_str[bam_seqi(bam_get_seq(bamdata),i)]) {
|
|
case 'A':
|
|
++cnt[0];
|
|
break;
|
|
case 'C':
|
|
++cnt[1];
|
|
break;
|
|
case 'G':
|
|
++cnt[2];
|
|
break;
|
|
case 'T':
|
|
++cnt[3];
|
|
break;
|
|
default: //N
|
|
++cnt[4];
|
|
break;
|
|
}
|
|
}
|
|
|
|
if (bam_aux_update_array(bamdata, "BA", 'I', sizeof(cnt)/sizeof(cnt[0]), cnt)) {
|
|
printf("Failed to update base array, errno %d", errno);
|
|
goto end;
|
|
}
|
|
|
|
if (sam_write1(outfile, in_samhdr, bamdata) < 0) {
|
|
printf("Failed to write output\n");
|
|
goto end;
|
|
}
|
|
}
|
|
if (ret_r < -1) {
|
|
//read error
|
|
printf("Failed to read data\n");
|
|
goto end;
|
|
}
|
|
|
|
ret = EXIT_SUCCESS;
|
|
end:
|
|
//cleanup
|
|
if (in_samhdr) {
|
|
sam_hdr_destroy(in_samhdr);
|
|
}
|
|
if (infile) {
|
|
sam_close(infile);
|
|
}
|
|
if (outfile) {
|
|
sam_close(outfile);
|
|
}
|
|
if (bamdata) {
|
|
bam_destroy1(bamdata);
|
|
}
|
|
return ret;
|
|
}
|