From: peterjc Date: Tue, 3 Apr 2012 14:23:36 +0000 (+0100) Subject: Support SAM or BAM input/output in 'samtools depad' (default still BAM -> BAM) X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=3d8051c6517ef1a21ee5b9925b432a17dc75f2d1 Support SAM or BAM input/output in 'samtools depad' (default still BAM -> BAM) --- diff --git a/padding.c b/padding.c index 9fbdb53..a10c08f 100644 --- a/padding.c +++ b/padding.c @@ -2,6 +2,8 @@ #include #include #include "kstring.h" +#include "sam_header.h" +#include "sam.h" #include "bam.h" static void replace_cigar(bam1_t *b, int n, uint32_t *cigar) @@ -66,21 +68,20 @@ static void unpad_seq(bam1_t *b, kstring_t *s) assert(length == s->l); } -int bam_pad2unpad(bamFile in, bamFile out) +int bam_pad2unpad(samfile_t *in, samfile_t *out) { bam_header_t *h; bam1_t *b; kstring_t r, q; int r_tid = -1; uint32_t *cigar2 = 0; - int n2 = 0, m2 = 0, *posmap = 0; + int ret = 0, n2 = 0, m2 = 0, *posmap = 0; - h = bam_header_read(in); - /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */ - bam_header_write(out, h); b = bam_init1(); r.l = r.m = q.l = q.m = 0; r.s = q.s = 0; - while (bam_read1(in, b) >= 0) { + int read_ret; + h = in->header; + while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in' uint32_t *cigar = bam1_cigar(b); n2 = 0; if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) { @@ -168,53 +169,92 @@ int bam_pad2unpad(bamFile in, bamFile out) replace_cigar(b, n2, cigar2); b->core.pos = posmap[b->core.pos]; } - bam_write1(out, b); + samwrite(out, b); + } + if (read_ret < -1) { + fprintf(stderr, "[depad] truncated file.\n"); + ret = 1; } free(r.s); free(q.s); free(posmap); bam_destroy1(b); - bam_header_destroy(h); - return 0; + return ret; } static int usage(int is_long_help); int main_pad2unpad(int argc, char *argv[]) { - bamFile in, out; - int c, is_long_help = 0; - int result=0; + samfile_t *in = 0, *out = 0; + int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0; + char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0; + int ret=0; /* parse command-line options */ - while ((c = getopt(argc, argv, "?")) >= 0) { + strcpy(in_mode, "r"); strcpy(out_mode, "w"); + while ((c = getopt(argc, argv, "Sso:u1?")) >= 0) { switch (c) { - case '?': is_long_help = 1; break; + case 'S': is_bamin = 0; break; + case 's': assert(compress_level == -1); is_bamout = 0; break; + case 'o': fn_out = strdup(optarg); break; + case 'u': assert(is_bamout == 1); compress_level = 0; break; + case '1': assert(is_bamout == 1); compress_level = 1; break; + case '?': is_long_help = 1; break; default: return usage(is_long_help); } } if (argc == optind) return usage(is_long_help); - in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r"); - out = bam_dopen(fileno(stdout), "w"); - result = bam_pad2unpad(in, out); - bam_close(in); bam_close(out); - return result; + if (is_bamin) strcat(in_mode, "b"); + if (is_bamout) strcat(out_mode, "b"); + strcat(out_mode, "h"); + if (compress_level >= 0) { + char tmp[2]; + tmp[0] = compress_level + '0'; tmp[1] = '\0'; + strcat(out_mode, tmp); + } + + // open file handlers + if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) { + fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]); + ret = 1; + goto depad_end; + } + if (in->header == 0) { + fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]); + ret = 1; + goto depad_end; + } + /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */ + if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) { + fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output"); + ret = 1; + goto depad_end; + } + + // Do the depad + ret = bam_pad2unpad(in, out); + +depad_end: + // close files, free and return + free(fn_list); free(fn_out); + samclose(in); + samclose(out); + return ret; } static int usage(int is_long_help) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools depad \n\n"); - fprintf(stderr, "Options: -? longer help\n"); - //TODO - These are the arguments I think make sense to support: - //fprintf(stderr, "Usage: samtools depad [options] |\n\n"); - //fprintf(stderr, "Options: -b output BAM\n"); - //fprintf(stderr, " -S input is SAM\n"); - //fprintf(stderr, " -u uncompressed BAM output (force -b)\n"); - //fprintf(stderr, " -1 fast compression (force -b)\n"); + fprintf(stderr, "Options: -s output is SAM (default is BAM)\n"); + fprintf(stderr, " -S input is SAM (default is BAM)\n"); + fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n"); + fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n"); + //TODO - These are the arguments I think make sense to support: //fprintf(stderr, " -@ INT number of BAM compression threads [0]\n"); //fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n"); - //fprintf(stderr, " -o FILE output file name [stdout]\n"); - //fprintf(stderr, " -? longer help\n"); + fprintf(stderr, " -o FILE output file name [stdout]\n"); + fprintf(stderr, " -? longer help\n"); fprintf(stderr, "\n"); if (is_long_help) fprintf(stderr, "Notes:\n\