X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=cbb55cc3a5a7d1643b729c63bd1c36ad206e6387;hb=6971381d1e639d69dd3d72f8f16e2726c95fd3e4;hp=1d5ea5a82da2076217deb9bf224a5ed12b0655ef;hpb=b0ed19dc2d8fb84998d41d6c3588611185707137;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index 1d5ea5a..cbb55cc 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -1,3 +1,4 @@ +#include #include #include #include @@ -15,6 +16,11 @@ 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 +#define BAM_PLF_2ND 0x20 +#define BAM_PLF_RANBASE 0x40 +#define BAM_PLF_1STBASE 0x80 +#define BAM_PLF_ALLBASE 0x100 typedef struct { bam_header_t *h; @@ -118,9 +124,11 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, g3->offset = pos - d->last_pos; d->last_pos = pos; glf3_write1(d->fp_glf, g3); - 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); + if (pos < d->len) { + 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); + } if (r) { // then write indel line int het = 3 * n, min; min = het; @@ -151,48 +159,86 @@ 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 + if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE)) { // use a random base or the 1st base as the consensus call + const bam_pileup1_t *p = (d->format & BAM_PLF_1STBASE)? pu : pu + (int)(drand48() * n); + int q = bam1_qual(p->b)[p->qpos]; + int mapQ = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ; + uint32_t b = bam1_seqi(bam1_seq(p->b), p->qpos); + cns = b<<28 | 0xf<<24 | mapQ<<16 | q<<8; + } else if (d->format & BAM_PLF_ALLBASE) { // collapse all bases + uint64_t rmsQ = 0; + uint32_t b = 0; + for (i = 0; i < n; ++i) { + const bam_pileup1_t *p = pu + i; + int q = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ; + b |= bam1_seqi(bam1_seq(p->b), p->qpos); + rmsQ += q * q; + } + rmsQ = (uint64_t)(sqrt((double)rmsQ / n) + .499); + cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8; + } else cns = bam_maqcns_call(n, pu, d->c); + } + if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // 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 + if (r) bam_maqindel_ret_destroy(r); + 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; + 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); } - 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); - } - // 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 +261,33 @@ 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); } + if (d->format & BAM_PLF_2ND) { // print 2nd calls and qualities + const unsigned char *q; + putchar('\t'); + for (i = 0; i < n; ++i) { + const bam_pileup1_t *p = pu + i; + q = bam_aux_get(p->b, "E2"); + putchar(q? q[p->qpos + 1] : 'N'); + } + putchar('\t'); + for (i = 0; i < n; ++i) { + const bam_pileup1_t *p = pu + i; + q = bam_aux_get(p->b, "U2"); + putchar(q? q[p->qpos + 1] : '!'); + } + } + // 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) { @@ -231,15 +297,18 @@ 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); + printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti); + printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi); bam_maqindel_ret_destroy(r); } return 0; @@ -247,14 +316,15 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p int bam_pileup(int argc, char *argv[]) { - int c; + int c, is_SAM = 0; char *fn_list = 0, *fn_fa = 0, *fn_pos = 0; pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t)); 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:S2aR:")) >= 0) { switch (c) { + case 'a': d->c->is_soap = 1; break; case 's': d->format |= BAM_PLF_SIMPLE; break; case 't': fn_list = strdup(optarg); break; case 'l': fn_pos = strdup(optarg); break; @@ -262,25 +332,41 @@ 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 '2': d->format |= BAM_PLF_2ND; break; case 'I': d->ido->q_indel = atoi(optarg); break; case 'G': d->ido->r_indel = atof(optarg); break; + case 'S': is_SAM = 1; break; + case 'R': + if (strcmp(optarg, "random") == 0) d->format |= BAM_PLF_RANBASE; + else if (strcmp(optarg, "first") == 0) d->format |= BAM_PLF_1STBASE; + else if (strcmp(optarg, "all") == 0) d->format |= BAM_PLF_ALLBASE; + else fprintf(stderr, "[bam_pileup] unrecognized -R\n"); + break; default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1; } } + if (fn_list) is_SAM = 1; if (optind == argc) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools pileup [options] |\n\n"); fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n"); + fprintf(stderr, " -S the input is in SAM\n"); + fprintf(stderr, " -a use the SOAPsnp model for SNP calling\n"); + fprintf(stderr, " -2 output the 2nd best call and quality\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, " -t FILE list of reference sequences (assume the input is in SAM)\n"); + fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ); + fprintf(stderr, " -t FILE list of reference sequences (force -S)\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); @@ -291,6 +377,7 @@ int bam_pileup(int argc, char *argv[]) free(fn_list); free(fn_fa); free(d); return 1; } + if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE|BAM_PLF_ALLBASE)) d->format |= BAM_PLF_CNS; if (fn_fa) d->fai = fai_load(fn_fa); if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling if (d->format & BAM_PLF_GLF) { // for glf output @@ -302,9 +389,11 @@ int bam_pileup(int argc, char *argv[]) } if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY))) fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n"); + if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa); + { samfile_t *fp; - fp = fn_list? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0); + fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0); if (fp == 0 || fp->header == 0) { fprintf(stderr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n"); return 1;