/* read_aux.c -- showcases the htslib api usage Copyright (C) 2023 Genome Research Ltd. Author: Vasudeva Sarma 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 #include #include /// 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: read_aux infile tag\n\ Read the given aux tag from alignments either as SAM string or as raw data\n"); } /// printauxdata - prints aux data /** @param fp - file to which it to be printed - stdout or null * @param type - aux type * @param idx - index in array, -1 when not an array type * @param data - data * recurses when the data is array type returns 1 on failure 0 on success */ int printauxdata(FILE *fp, char type, int32_t idx, const uint8_t *data) { uint32_t auxBcnt = 0; int i = 0; char auxBType = 'Z'; //the tag is already queried and ensured to exist and the type is retrieved from the tag data, also iterated within index for arrays, so no error is expected here. //when these apis are used explicitly, these error conditions needs to be handled based on return value and errno switch(type) { case 'A': fprintf(fp, "%c", bam_aux2A(data)); //byte data break; case 'c': fprintf(fp, "%d", (int8_t)(idx > -1 ? bam_auxB2i(data, idx) : bam_aux2i(data))); //signed 1 byte data; bam_auxB2i - from array or bam_aux2i - non array data break; case 'C': fprintf(fp, "%u", (uint8_t)(idx > -1 ? bam_auxB2i(data, idx) : bam_aux2i(data))); //unsigned 1 byte data break; case 's': fprintf(fp, "%d", (int16_t)(idx > -1 ? bam_auxB2i(data, idx) : bam_aux2i(data))); //signed 2 byte data break; case 'S': fprintf(fp, "%u", (uint16_t)(idx > -1 ? bam_auxB2i(data, idx) : bam_aux2i(data))); //unsigned 2 byte data break; case 'i': fprintf(fp, "%d", (int32_t)(idx > -1 ? bam_auxB2i(data, idx) : bam_aux2i(data))); //signed 4 byte data break; case 'I': fprintf(fp, "%u", (uint32_t)(idx > -1 ? bam_auxB2i(data, idx) : bam_aux2i(data))); //unsigned 4 byte data break; case 'f': case 'd': fprintf(fp, "%g", (float)(idx > -1 ? bam_auxB2f(data, idx) : bam_aux2f(data))); //floating point data, 4 bytes break; case 'H': case 'Z': fprintf(fp, "%s", bam_aux2Z(data)); //array of char or hex data break; case 'B': //array of char/int/float auxBcnt = bam_auxB_len(data); //length of array auxBType = bam_aux_type(data + 1); //type of element in array fprintf(fp, "%c", auxBType); for (i = 0; i < auxBcnt; ++i) { //iterate the array fprintf(fp, ","); //calling recurssively with index to reuse a few lines if (printauxdata(fp, auxBType, i, data) == EXIT_FAILURE) { return EXIT_FAILURE; } } break; default: printf("Invalid aux tag?\n"); return EXIT_FAILURE; break; } return EXIT_SUCCESS; } /// 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; int c = 0, ret = EXIT_FAILURE, ret_r = 0, i = 0; sam_hdr_t *in_samhdr = NULL; samFile *infile = NULL; bam1_t *bamdata = NULL; uint8_t *data = NULL; kstring_t sdata = KS_INITIALIZE; //read_aux infile tag if (argc != 3) { print_usage(stderr); goto end; } inname = argv[1]; tag = argv[2]; 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; } if (!(in_samhdr = sam_hdr_read(infile))) { printf("Failed to read header from file!\n"); goto end; } while ((ret_r = sam_read1(infile, in_samhdr, bamdata)) >= 0) { errno = 0; i++; ks_clear(&sdata); if (i % 2) { //use options alternatively to demonstrate both //option 1 - get data as string with tag and type if ((c = bam_aux_get_str(bamdata, tag, &sdata)) == 1) { printf("%s\n",sdata.s); } else if (c == 0 && errno == ENOENT) { //tag not present printf("Tag not present\n"); } else { //error printf("Failed to get tag\n"); goto end; } } else { //option 2 - get raw data if (!(data = bam_aux_get(bamdata, tag))) { //tag data not returned, errono gives the reason if (errno == ENOENT) { printf("Tag not present\n"); } else { printf("Invalid aux data\n"); } } else { //got the tag, read and print if (printauxdata(stdout, bam_aux_type(data), -1, data) == EXIT_FAILURE) { printf("Failed to read aux data\n"); goto end; } printf("\n"); } } } 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 (bamdata) { bam_destroy1(bamdata); } ks_free(&sdata); return ret; }