From 4c4b72301b736e08e37b5e0dd1d435477d969898 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 8 Jun 2009 10:11:06 +0000 Subject: [PATCH 1/1] * samtools-0.1.4-2 (r316) * pileup: cap mapping quality at 60 (by default) * pileup: always calculate RMS mapq * pileup: allow to output variant sites only --- bam_maqcns.c | 5 +++- bam_maqcns.h | 2 +- bam_plcmd.c | 71 +++++++++++++++++++++++++++++++++++++--------------- bamtk.c | 2 +- sam.c | 2 +- 5 files changed, 58 insertions(+), 24 deletions(-) diff --git a/bam_maqcns.c b/bam_maqcns.c index c6c9af7..95cd2b5 100644 --- a/bam_maqcns.c +++ b/bam_maqcns.c @@ -108,6 +108,7 @@ bam_maqcns_t *bam_maqcns_init() bm->theta = 0.85; bm->n_hap = 2; bm->eta = 0.03; + bm->cap_mapQ = 60; return bm; } @@ -160,6 +161,7 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam rms = 0; for (j = n - 1; j >= 0; --j) { // calculate esum and fsum uint32_t info = bm->aux->info[j]; + int tmp; if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | (info&0xffffff); k = info>>16&7; if (info>>24 > 0) { @@ -168,7 +170,8 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam if (w[k] < 0xff) ++w[k]; ++b->c[k&3]; } - rms += (int)(info&0x7f) * (info&0x7f); + tmp = (int)(info&0x7f) < bm->cap_mapQ? (int)(info&0x7f) : bm->cap_mapQ; + rms += tmp * tmp; } b->rms_mapQ = (uint8_t)(sqrt((double)rms / n) + .499); // rescale ->c[] diff --git a/bam_maqcns.h b/bam_maqcns.h index 56fa9db..36704d7 100644 --- a/bam_maqcns.h +++ b/bam_maqcns.h @@ -7,7 +7,7 @@ struct __bmc_aux_t; typedef struct { float het_rate, theta; - int n_hap; + int n_hap, cap_mapQ; float eta, q_r; double *fk, *coef; diff --git a/bam_plcmd.c b/bam_plcmd.c index 1d5ea5a..46f078a 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -1,3 +1,4 @@ +#include #include #include #include @@ -15,6 +16,7 @@ KHASH_MAP_INIT_INT64(64, indel_list_t) #define BAM_PLF_CNS 0x02 #define BAM_PLF_INDEL_ONLY 0x04 #define BAM_PLF_GLF 0x08 +#define BAM_PLF_VAR_ONLY 0x10 typedef struct { bam_header_t *h; @@ -151,48 +153,66 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p { pu_data_t *d = (pu_data_t*)data; bam_maqindel_ret_t *r = 0; - int i, j, rb, rms_mapq = -1, max_mapq = 0, *proposed_indels = 0; - uint32_t x; + int i, j, rb, rms_mapq = -1, *proposed_indels = 0; + uint64_t rms_aux; + uint32_t cns = 0; + // if GLF is required, suppress -c completely if (d->format & BAM_PLF_GLF) return glt3_func(tid, pos, n, pu, data); - if (d->hash) { // only output a list of sites + // if d->hash is initialized, only output the sites in the hash table + if (d->hash) { khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos); if (k == kh_end(d->hash)) return 0; proposed_indels = kh_val(d->hash, k); } - if (d->fai && (int)tid != d->tid) { // then update d->ref + // update d->ref if necessary + if (d->fai && (int)tid != d->tid) { free(d->ref); d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len); d->tid = tid; } rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N'; + // when the indel-only mode is asked for, return if no reads mapped with indels if (d->format & BAM_PLF_INDEL_ONLY) { for (i = 0; i < n; ++i) if (pu[i].indel != 0) break; if (i == n) return 0; } + // call the consensus and indel + if (d->format & BAM_PLF_CNS) // call consensus + cns = bam_maqcns_call(n, pu, d->c); + if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { // call indels + if (proposed_indels) // the first element gives the size of the array + r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); + else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0); + } + // when only variant sites are asked for, test if the site is a variant + if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) { + if (!(bam_nt16_table[rb] != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP + if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) // not an indel + return 0; + } + } + // print the first 3 columns printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb); - if (d->format & BAM_PLF_CNS) { // consensus + // print consensus information if required + if (d->format & BAM_PLF_CNS) { int ref_q, rb4 = bam_nt16_table[rb]; - x = bam_maqcns_call(n, pu, d->c); ref_q = 0; - if (rb4 != 15 && x>>28 != 15 && x>>28 != rb4) { // a SNP - ref_q = ((x>>24&0xf) == rb4)? x>>8&0xff : (x>>8&0xff) + (x&0xff); + if (rb4 != 15 && cns>>28 != 15 && cns>>28 != rb4) { // a SNP + ref_q = ((cns>>24&0xf) == rb4)? cns>>8&0xff : (cns>>8&0xff) + (cns&0xff); if (ref_q > 255) ref_q = 255; } - printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[x>>28], x>>8&0xff, ref_q, x>>16&0xff); - rms_mapq = x>>16&0xff; - } - if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { - if (proposed_indels) - r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); - else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0); + rms_mapq = cns>>16&0xff; + printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, ref_q, rms_mapq); } - // pileup strings + // print pileup sequences printf("%d\t", n); + rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pu + i; - if (max_mapq < p->b->core.qual) max_mapq = p->b->core.qual; + int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ; + rms_aux += tmp * tmp; if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33); if (!p->is_del) { int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; @@ -215,13 +235,18 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p } else putchar('*'); if (p->is_tail) putchar('$'); } + // finalize rms_mapq + rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499); + if (rms_mapq < 0) rms_mapq = rms_aux; putchar('\t'); + // print quality for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pu + i; int c = bam1_qual(p->b)[p->qpos] + 33; if (c > 126) c = 126; putchar(c); } + // print mapping quality if -s is flagged on the command line if (d->format & BAM_PLF_SIMPLE) { putchar('\t'); for (i = 0; i < n; ++i) { @@ -231,12 +256,14 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p } } putchar('\n'); - if (r) { // then print indel line + // print the indel line if r has been calculated. This only happens if: + // a) -c or -i are flagged, AND b) the reference sequence is available + if (r) { printf("%s\t%d\t*\t", d->h->target_name[tid], pos + 1); if (r->gt < 2) printf("%s/%s\t", r->s[r->gt], r->s[r->gt]); else printf("%s/%s\t", r->s[0], r->s[1]); printf("%d\t%d\t", r->q_cns, r->q_ref); - printf("%d\t%d\t", rms_mapq >= 0? rms_mapq : max_mapq, n); + printf("%d\t%d\t", rms_mapq, n); printf("%s\t%s\t", r->s[0], r->s[1]); //printf("%d\t%d\t", r->gl[0], r->gl[1]); printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti); @@ -253,7 +280,7 @@ int bam_pileup(int argc, char *argv[]) d->tid = -1; d->mask = BAM_DEF_MASK; d->c = bam_maqcns_init(); d->ido = bam_maqindel_opt_init(); - while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:")) >= 0) { + while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:")) >= 0) { switch (c) { case 's': d->format |= BAM_PLF_SIMPLE; break; case 't': fn_list = strdup(optarg); break; @@ -262,8 +289,10 @@ int bam_pileup(int argc, char *argv[]) case 'T': d->c->theta = atof(optarg); break; case 'N': d->c->n_hap = atoi(optarg); break; case 'r': d->c->het_rate = atof(optarg); break; + case 'M': d->c->cap_mapQ = atoi(optarg); break; case 'c': d->format |= BAM_PLF_CNS; break; case 'i': d->format |= BAM_PLF_INDEL_ONLY; break; + case 'v': d->format |= BAM_PLF_VAR_ONLY; break; case 'm': d->mask = strtol(optarg, 0, 0); break; case 'g': d->format |= BAM_PLF_GLF; break; case 'I': d->ido->q_indel = atoi(optarg); break; @@ -277,10 +306,12 @@ int bam_pileup(int argc, char *argv[]) fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n"); fprintf(stderr, " -i only show lines/consensus with indels\n"); fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask); + fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ); fprintf(stderr, " -t FILE list of reference sequences (assume the input is in SAM)\n"); fprintf(stderr, " -l FILE list of sites at which pileup is output\n"); fprintf(stderr, " -f FILE reference sequence in the FASTA format\n\n"); fprintf(stderr, " -c output the maq consensus sequence\n"); + fprintf(stderr, " -v print variants only (for -c)\n"); fprintf(stderr, " -g output in the GLFv3 format (suppressing -c/-i/-s)\n"); fprintf(stderr, " -T FLOAT theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta); fprintf(stderr, " -N INT number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap); diff --git a/bamtk.c b/bamtk.c index 9b3aae1..0fb7cb4 100644 --- a/bamtk.c +++ b/bamtk.c @@ -3,7 +3,7 @@ #include "bam.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.4-1 (r304)" +#define PACKAGE_VERSION "0.1.4-2 (r316)" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/sam.c b/sam.c index 8411d81..48a4b34 100644 --- a/sam.c +++ b/sam.c @@ -43,7 +43,7 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux) fp->header = sam_header_read2((const char*)aux); } if (fp->header->n_targets == 0) - fprintf(stderr, "[samopen] empty header.\n"); + fprintf(stderr, "[samopen] no @SQ lines in the header.\n"); } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets); } } else if (mode[0] == 'w') { // write -- 2.39.2