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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,220 @@ | ||
| /* mod_aux.c -- showcases the htslib api usage | ||
| Copyright (C) 2023 Genome Research Ltd. | ||
| Author: Vasudeva Sarma <[email protected]> | ||
| 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 pupose of this code is to demonstrate the library apis and need proper error handling and optimization */ | ||
|
|
||
| #include <getopt.h> | ||
| #include <unistd.h> | ||
| #include <htslib/sam.h> | ||
|
|
||
| /// print_usage - print the demo_usage | ||
| /** @param fp pointer to the file / terminal to which demo_usage to be dumped | ||
| returns nothing | ||
| */ | ||
| static void print_usage(FILE *fp) | ||
| { | ||
| fprintf(fp, "Usage: mod_aux infile QNAME tag type val\n\ | ||
| Add/update the given aux tag to all alignments\n\ | ||
| type A-char C-int F-float Z-string\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, *tag = NULL, *qname = NULL, *val = NULL; | ||
| char type = '\0'; | ||
| int c = 0, ret = EXIT_FAILURE, ret_r = 0, length = 0; | ||
| sam_hdr_t *in_samhdr = NULL; | ||
| samFile *infile = NULL, *outfile = NULL; | ||
| bam1_t *bamdata = NULL; | ||
| uint8_t *data = NULL; | ||
|
|
||
| //mod_aux infile QNAME tag type val | ||
| if (argc != 6) { | ||
| print_usage(stderr); | ||
| goto end; | ||
| } | ||
| inname = argv[1]; | ||
| qname = argv[2]; | ||
| tag = argv[3]; | ||
| type = argv[4][0]; | ||
| val = argv[5]; | ||
|
|
||
| if (type >= 'a' && type <='z') { | ||
| type -= 32; //make it upper case | ||
| } | ||
| 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) { | ||
| if (strcasecmp(bam_get_qname(bamdata), qname)) { | ||
| if (sam_write1(outfile, in_samhdr, bamdata) < 0) { | ||
| printf("Failed to write output\n"); | ||
| goto end; | ||
| } | ||
| continue; //not matching | ||
| } | ||
|
|
||
| errno = 0; | ||
| //matched to qname, update aux | ||
| if (!(data = bam_aux_get(bamdata, tag))) { | ||
| int i = 0; float f = 0; | ||
| //tag not present append | ||
| switch (type) { | ||
| case 'F': | ||
| case 'D': | ||
| length = sizeof(float); | ||
| f = atof(val); | ||
| val = (const char*) &f; | ||
| break; | ||
| case 'C': | ||
| case 'S': | ||
| case 'I': | ||
| length = sizeof(int); | ||
| i = atoi(val); | ||
| val = (const char*) &i; | ||
| break; | ||
| case 'Z': | ||
| length = strlen(val) + 1; //1 for NUL termination | ||
| break; | ||
| case 'A': | ||
| length = 1; | ||
| break; | ||
| } | ||
| if (bam_aux_append(bamdata, tag, type, length, (const uint8_t*)val)) { | ||
| printf("Failed to append aux data, errno: %d\n", errno); | ||
| goto end; | ||
| } | ||
| } | ||
| else { | ||
| char auxtype = bam_aux_type(data); | ||
| //update the tag with newer value | ||
| switch (type) { | ||
| case 'F': | ||
| case 'D': | ||
| if (auxtype != 'f' && auxtype != 'd') { | ||
| printf("Invalid aux type passed\n"); | ||
| goto end; | ||
| } | ||
| if (bam_aux_update_float(bamdata, tag, atof(val))) { | ||
| printf("Failed to update float data, errno: %d\n", errno); | ||
| goto end; | ||
| } | ||
| break; | ||
| case 'C': | ||
| case 'S': | ||
| case 'I': | ||
| if (auxtype != 'c' && auxtype != 'C' && auxtype != 's' && auxtype != 'S' && auxtype != 'i' && auxtype != 'I') { | ||
| printf("Invalid aux type passed\n"); | ||
| goto end; | ||
| } | ||
| if (bam_aux_update_int(bamdata, tag, atoll(val))) { | ||
| printf("Failed to update int data, errno: %d\n", errno); | ||
| goto end; | ||
| } | ||
| break; | ||
| case 'Z': | ||
| if (auxtype != 'Z') { | ||
| printf("Invalid aux type passed\n"); | ||
| goto end; | ||
| } | ||
| length = strlen(val) + 1; //1 for NUL termination | ||
| if (bam_aux_update_str(bamdata, tag, length, val)) { | ||
| //with length as -1, length will be detected based on null terminated val data | ||
| printf("Failed to update string data, errno: %d\n", errno); | ||
| goto end; | ||
| } | ||
| break; | ||
| case 'A': | ||
| if (auxtype != 'A') { | ||
| printf("Invalid aux type passed\n"); | ||
| goto end; | ||
| } | ||
| //update the char data directly on buffer | ||
| *(data+1) = val[0]; | ||
| break; | ||
| //TODO there is no H update support! | ||
| default: | ||
| printf("Invalid data type\n"); | ||
| goto end; | ||
| break; | ||
| } | ||
| } | ||
| 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; | ||
| } |
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