X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_plcmd.c;h=fd75cec8c8841a1f174731dc2eeef603571b86d2;hp=dca85181f99bf1c7343650846039153a019e7ea9;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522 diff --git a/bam_plcmd.c b/bam_plcmd.c index dca8518..fd75cec 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -2,6 +2,8 @@ #include #include #include +#include +#include #include "sam.h" #include "faidx.h" #include "bam_maqcns.h" @@ -528,19 +530,28 @@ int bam_pileup(int argc, char *argv[]) #define MPLP_NO_COMP 0x20 #define MPLP_NO_ORPHAN 0x40 #define MPLP_REALN 0x80 +#define MPLP_FMT_DP 0x100 +#define MPLP_FMT_SP 0x200 +#define MPLP_NO_INDEL 0x400 +#define MPLP_EXT_BAQ 0x800 +#define MPLP_ILLUMINA13 0x1000 typedef struct { - int max_mq, min_mq, flag, min_baseQ, capQ_thres; - char *reg, *fn_pos; + int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth; + int openQ, extQ, tandemQ, min_support; // for indels + double min_frac; // for indels + char *reg, *fn_pos, *pl_list; faidx_t *fai; kh_64_t *hash; + void *rghash; } mplp_conf_t; typedef struct { bamFile fp; bam_iter_t iter; - int min_mq, flag, ref_id, capQ_thres; + int ref_id; char *ref; + const mplp_conf_t *conf; } mplp_aux_t; typedef struct { @@ -552,23 +563,35 @@ typedef struct { static int mplp_func(void *data, bam1_t *b) { extern int bam_realn(bam1_t *b, const char *ref); - extern int bam_prob_realn(bam1_t *b, const char *ref); + extern int bam_prob_realn_core(bam1_t *b, const char *ref, int); extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres); mplp_aux_t *ma = (mplp_aux_t*)data; int ret, skip = 0; do { - int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; + int has_ref; ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b); if (ret < 0) break; + if (ma->conf->rghash) { // exclude read groups + uint8_t *rg = bam_aux_get(b, "RG"); + skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0); + if (skip) continue; + } + if (ma->conf->flag & MPLP_ILLUMINA13) { + int i; + uint8_t *qual = bam1_qual(b); + for (i = 0; i < b->core.l_qseq; ++i) + qual[i] = qual[i] > 31? qual[i] - 31 : 0; + } + has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; skip = 0; - if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn(b, ma->ref); - if (has_ref && ma->capQ_thres > 10) { - int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres); + if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1); + if (has_ref && ma->conf->capQ_thres > 10) { + int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres); if (q < 0) skip = 1; else if (b->core.qual > q) b->core.qual = q; } else if (b->core.flag&BAM_FUNMAP) skip = 1; - else if (b->core.qual < ma->min_mq) skip = 1; - else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1; + else if (b->core.qual < ma->conf->min_mq) skip = 1; + else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1; } while (skip); return ret; } @@ -598,13 +621,16 @@ static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf, static int mpileup(mplp_conf_t *conf, int n, char **fn) { + extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list); + extern void bcf_call_del_rghash(void *rghash); mplp_aux_t **data; - int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid; + int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth, max_indel_depth; const bam_pileup1_t **plp; bam_mplp_t iter; bam_header_t *h = 0; char *ref; khash_t(64) *hash = 0; + void *rghash = 0; bcf_callaux_t *bca = 0; bcf_callret1_t *bcr = 0; @@ -628,12 +654,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) for (i = 0; i < n; ++i) { bam_header_t *h_tmp; data[i] = calloc(1, sizeof(mplp_aux_t)); - data[i]->min_mq = conf->min_mq; - data[i]->flag = conf->flag; - data[i]->capQ_thres = conf->capQ_thres; data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r"); + data[i]->conf = conf; h_tmp = bam_header_read(data[i]->fp); bam_smpl_add(sm, fn[i], h_tmp->text); + rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list); if (conf->reg) { int beg, end; bam_index_t *idx; @@ -683,15 +708,29 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) bh->l_smpl = s.l; bh->sname = malloc(s.l); memcpy(bh->sname, s.s, s.l); - bh->l_txt = 0; + bh->txt = malloc(strlen(BAM_VERSION) + 64); + bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION); free(s.s); bcf_hdr_sync(bh); bcf_hdr_write(bp, bh); bca = bcf_call_init(-1., conf->min_baseQ); bcr = calloc(sm->n, sizeof(bcf_callret1_t)); + bca->rghash = rghash; + bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ; + bca->min_frac = conf->min_frac; + bca->min_support = conf->min_support; } ref_tid = -1; ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); + max_depth = conf->max_depth; + if (max_depth * sm->n > 1<<20) + fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__); + if (max_depth * sm->n < 8000) { + max_depth = 8000 / sm->n; + fprintf(stderr, "<%s> Set max per-sample depth to %d\n", __func__, max_depth); + } + max_indel_depth = conf->max_indel_depth * sm->n; + bam_mplp_set_maxcnt(iter, max_depth); while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) { if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested if (hash) { @@ -706,17 +745,31 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) ref_tid = tid; } if (conf->flag & MPLP_GLF) { - int _ref0, ref16; + int total_depth, _ref0, ref16; bcf1_t *b = calloc(1, sizeof(bcf1_t)); + for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i]; group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp); _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; ref16 = bam_nt16_table[_ref0]; for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); bcf_call_combine(gplp.n, bcr, ref16, &bc); - bcf_call2bcf(tid, pos, &bc, b); + bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, + (conf->flag&MPLP_FMT_SP), 0, 0); bcf_write(bp, bh, b); bcf_destroy(b); + // call indels + if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) { + for (i = 0; i < gplp.n; ++i) + bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); + if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) { + b = calloc(1, sizeof(bcf1_t)); + bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, + (conf->flag&MPLP_FMT_SP), bca, ref); + bcf_write(bp, bh, b); + bcf_destroy(b); + } + } } else { printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < n; ++i) { @@ -743,6 +796,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) bam_smpl_destroy(sm); free(buf.s); for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); + bcf_call_del_rghash(rghash); if (hash) { // free the hash table khint_t k; for (k = kh_begin(hash); k < kh_end(hash); ++k) @@ -761,53 +815,156 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) return 0; } +#define MAX_PATH_LEN 1024 +static int read_file_list(const char *file_list,int *n,char **argv[]) +{ + char buf[MAX_PATH_LEN]; + int len, nfiles; + char **files; + + FILE *fh = fopen(file_list,"r"); + if ( !fh ) + { + fprintf(stderr,"%s: %s\n", file_list,strerror(errno)); + return 1; + } + + // Speed is not an issue here, determine the number of files by reading the file twice + nfiles = 0; + while ( fgets(buf,MAX_PATH_LEN,fh) ) nfiles++; + + if ( fseek(fh, 0L, SEEK_SET) ) + { + fprintf(stderr,"%s: %s\n", file_list,strerror(errno)); + return 1; + } + + files = calloc(nfiles,sizeof(char*)); + nfiles = 0; + while ( fgets(buf,MAX_PATH_LEN,fh) ) + { + len = strlen(buf); + while ( len>0 && isspace(buf[len-1]) ) len--; + if ( !len ) continue; + + files[nfiles] = malloc(sizeof(char)*(len+1)); + strncpy(files[nfiles],buf,len); + files[nfiles][len] = 0; + nfiles++; + } + fclose(fh); + if ( !nfiles ) + { + fprintf(stderr,"No files read from %s\n", file_list); + return 1; + } + *argv = files; + *n = nfiles; + return 0; +} +#undef MAX_PATH_LEN + int bam_mpileup(int argc, char *argv[]) { int c; + const char *file_list = NULL; + char **fn = NULL; + int nfiles = 0, use_orphan = 0; mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.max_mq = 60; mplp.min_baseQ = 13; mplp.capQ_thres = 0; + mplp.max_depth = 250; mplp.max_indel_depth = 250; + mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100; + mplp.min_frac = 0.002; mplp.min_support = 1; mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN; - while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:B")) >= 0) { + while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6")) >= 0) { switch (c) { case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == 0) return 1; break; + case 'd': mplp.max_depth = atoi(optarg); break; case 'r': mplp.reg = strdup(optarg); break; case 'l': mplp.fn_pos = strdup(optarg); break; + case 'P': mplp.pl_list = strdup(optarg); break; case 'g': mplp.flag |= MPLP_GLF; break; case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break; case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break; - case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break; - case 'O': mplp.flag |= MPLP_NO_ORPHAN; break; + case 'B': mplp.flag &= ~MPLP_REALN; break; case 'R': mplp.flag |= MPLP_REALN; break; + case 'D': mplp.flag |= MPLP_FMT_DP; break; + case 'S': mplp.flag |= MPLP_FMT_SP; break; + case 'I': mplp.flag |= MPLP_NO_INDEL; break; + case 'E': mplp.flag |= MPLP_EXT_BAQ; break; + case '6': mplp.flag |= MPLP_ILLUMINA13; break; case 'C': mplp.capQ_thres = atoi(optarg); break; case 'M': mplp.max_mq = atoi(optarg); break; case 'q': mplp.min_mq = atoi(optarg); break; case 'Q': mplp.min_baseQ = atoi(optarg); break; + case 'b': file_list = optarg; break; + case 'o': mplp.openQ = atoi(optarg); break; + case 'e': mplp.extQ = atoi(optarg); break; + case 'h': mplp.tandemQ = atoi(optarg); break; + case 'A': use_orphan = 1; break; + case 'F': mplp.min_frac = atof(optarg); break; + case 'm': mplp.min_support = atoi(optarg); break; + case 'L': mplp.max_indel_depth = atoi(optarg); break; + case 'G': { + FILE *fp_rg; + char buf[1024]; + mplp.rghash = bcf_str2id_init(); + if ((fp_rg = fopen(optarg, "r")) == 0) + fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg); + while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me... + bcf_str2id_add(mplp.rghash, strdup(buf)); + fclose(fp_rg); + } + break; } } + if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; if (argc == 1) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n"); fprintf(stderr, "Options: -f FILE reference sequence file [null]\n"); fprintf(stderr, " -r STR region in which pileup is generated [null]\n"); fprintf(stderr, " -l FILE list of positions (format: chr pos) [null]\n"); + fprintf(stderr, " -b FILE list of input BAM files [null]\n"); fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq); fprintf(stderr, " -Q INT min base quality [%d]\n", mplp.min_baseQ); fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq); + fprintf(stderr, " -d INT max per-BAM depth [%d]\n", mplp.max_depth); + fprintf(stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth); + fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n"); + fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ); + fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ); + fprintf(stderr, " -h INT coefficient for homopolyer errors [%d]\n", mplp.tandemQ); + fprintf(stderr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support); + fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac); + fprintf(stderr, " -G FILE exclude read groups listed in FILE [null]\n"); + fprintf(stderr, " -6 quality is in the Illumina-1.3+ encoding\n"); + fprintf(stderr, " -A use anomalous read pairs in SNP/INDEL calling\n"); fprintf(stderr, " -g generate BCF output\n"); fprintf(stderr, " -u do not compress BCF output\n"); + fprintf(stderr, " -E extended BAQ for higher sensitivity but lower specificity\n"); fprintf(stderr, " -B disable BAQ computation\n"); + fprintf(stderr, " -D output per-sample DP\n"); + fprintf(stderr, " -S output per-sample SP (strand bias P-value, slow)\n"); + fprintf(stderr, " -I do not perform indel calling\n"); fprintf(stderr, "\n"); fprintf(stderr, "Notes: Assuming diploid individuals.\n\n"); return 1; } - mpileup(&mplp, argc - optind, argv + optind); - free(mplp.reg); + if (file_list) { + if ( read_file_list(file_list,&nfiles,&fn) ) return 1; + mpileup(&mplp,nfiles,fn); + for (c=0; c