#include <errno.h>
#include "sam.h"
#include "faidx.h"
+#include "bam_maqcns.h"
+#include "khash.h"
+#include "glf.h"
#include "kstring.h"
+typedef int *indel_list_t;
+KHASH_MAP_INIT_INT64(64, indel_list_t)
+
+#define BAM_PLF_SIMPLE 0x01
+#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
+#define BAM_PLF_READPOS 0x200
+#define BAM_PLF_NOBAQ 0x400
+
+typedef struct {
+ bam_header_t *h;
+ bam_maqcns_t *c;
+ bam_maqindel_opt_t *ido;
+ faidx_t *fai;
+ khash_t(64) *hash;
+ uint32_t format;
+ int tid, len, last_pos;
+ int mask;
+ int capQ_thres, min_baseQ;
+ int max_depth; // for indel calling, ignore reads with the depth too high. 0 for unlimited
+ char *ref;
+ glfFile fp_glf; // for glf output only
+} pu_data_t;
+
+char **__bam_get_lines(const char *fn, int *_n);
+void bam_init_header_hash(bam_header_t *header);
+int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
+
+static khash_t(64) *load_pos(const char *fn, bam_header_t *h)
+{
+ char **list;
+ int i, j, n, *fields, max_fields;
+ khash_t(64) *hash;
+ bam_init_header_hash(h);
+ list = __bam_get_lines(fn, &n);
+ hash = kh_init(64);
+ max_fields = 0; fields = 0;
+ for (i = 0; i < n; ++i) {
+ char *str = list[i];
+ int chr, n_fields, ret;
+ khint_t k;
+ uint64_t x;
+ n_fields = ksplit_core(str, 0, &max_fields, &fields);
+ if (n_fields < 2) continue;
+ chr = bam_get_tid(h, str + fields[0]);
+ if (chr < 0) {
+ fprintf(pysamerr, "[load_pos] unknown reference sequence name: %s\n", str + fields[0]);
+ continue;
+ }
+ x = (uint64_t)chr << 32 | (atoi(str + fields[1]) - 1);
+ k = kh_put(64, hash, x, &ret);
+ if (ret == 0) {
+ fprintf(pysamerr, "[load_pos] position %s:%s has been loaded.\n", str+fields[0], str+fields[1]);
+ continue;
+ }
+ kh_val(hash, k) = 0;
+ if (n_fields > 2) {
+ // count
+ for (j = 2; j < n_fields; ++j) {
+ char *s = str + fields[j];
+ if ((*s != '+' && *s != '-') || !isdigit(s[1])) break;
+ }
+ if (j > 2) { // update kh_val()
+ int *q, y, z;
+ q = kh_val(hash, k) = (int*)calloc(j - 1, sizeof(int));
+ q[0] = j - 2; z = j; y = 1;
+ for (j = 2; j < z; ++j)
+ q[y++] = atoi(str + fields[j]);
+ }
+ }
+ free(str);
+ }
+ free(list); free(fields);
+ return hash;
+}
+
static inline int printw(int c, FILE *fp)
{
char buf[16];
return 0;
}
+// an analogy to pileup_func() below
+static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
+{
+ pu_data_t *d = (pu_data_t*)data;
+ bam_maqindel_ret_t *r = 0;
+ int rb, *proposed_indels = 0;
+ glf1_t *g;
+ glf3_t *g3;
+
+ if (d->fai == 0) {
+ fprintf(pysamerr, "[glt3_func] reference sequence is required for generating GLT. Abort!\n");
+ exit(1);
+ }
+ if (d->hash) { // only output a list of sites
+ 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);
+ }
+ g3 = glf3_init1();
+ if (d->fai && (int)tid != d->tid) {
+ if (d->ref) { // then write the end mark
+ g3->rtype = GLF3_RTYPE_END;
+ glf3_write1(d->fp_glf, g3);
+ }
+ glf3_ref_write(d->fp_glf, d->h->target_name[tid], d->h->target_len[tid]); // write reference
+ free(d->ref);
+ d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
+ d->tid = tid;
+ d->last_pos = 0;
+ }
+ rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
+ g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
+ memcpy(g3, g, sizeof(glf1_t));
+ g3->rtype = GLF3_RTYPE_SUB;
+ g3->offset = pos - d->last_pos;
+ d->last_pos = pos;
+ glf3_write1(d->fp_glf, g3);
+ if (pos < d->len) {
+ int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
+ if (proposed_indels)
+ r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+ else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
+ }
+ if (r) { // then write indel line
+ int het = 3 * n, min;
+ min = het;
+ if (min > r->gl[0]) min = r->gl[0];
+ if (min > r->gl[1]) min = r->gl[1];
+ g3->ref_base = 0;
+ g3->rtype = GLF3_RTYPE_INDEL;
+ memset(g3->lk, 0, 10);
+ g3->lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
+ g3->lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
+ g3->lk[2] = het - min < 255? het - min : 255;
+ g3->offset = 0;
+ g3->indel_len[0] = r->indel1;
+ g3->indel_len[1] = r->indel2;
+ g3->min_lk = min < 255? min : 255;
+ g3->max_len = (abs(r->indel1) > abs(r->indel2)? abs(r->indel1) : abs(r->indel2)) + 1;
+ g3->indel_seq[0] = strdup(r->s[0]+1);
+ g3->indel_seq[1] = strdup(r->s[1]+1);
+ glf3_write1(d->fp_glf, g3);
+ bam_maqindel_ret_destroy(r);
+ }
+ free(g);
+ glf3_destroy1(g3);
+ return 0;
+}
+
static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
{
int j;
if (p->is_tail) putchar('$');
}
+static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
+{
+ pu_data_t *d = (pu_data_t*)data;
+ bam_maqindel_ret_t *r = 0;
+ int i, 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 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);
+ }
+ // update d->ref if necessary
+ if (d->fai && (int)tid != d->tid) {
+ free(d->ref);
+ d->ref = faidx_fetch_seq(d->fai, d->h->target_name[tid], 0, 0x7fffffff, &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 {
+ glf1_t *g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
+ cns = g->depth == 0? (0xfu<<28 | 0xf<<24) : glf2cns(g, (int)(d->c->q_r + .499));
+ free(g);
+ }
+ }
+ if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
+ int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
+ if (proposed_indels) // the first element gives the size of the array
+ r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+ else r = bam_maqindel(m, 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 != 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
+ fputs(d->h->target_name[tid], stdout); putchar('\t');
+ printw(pos+1, stdout); putchar('\t'); putchar(rb); putchar('\t');
+ // print consensus information if required
+ if (d->format & BAM_PLF_CNS) {
+ putchar(bam_nt16_rev_table[cns>>28]); putchar('\t');
+ printw(cns>>8&0xff, stdout); putchar('\t');
+ printw(cns&0xff, stdout); putchar('\t');
+ printw(cns>>16&0xff, stdout); putchar('\t');
+ }
+ // print pileup sequences
+ printw(n, stdout); putchar('\t');
+ for (i = 0; i < n; ++i)
+ pileup_seq(pu + i, pos, d->len, d->ref);
+ // finalize rms_mapq
+ if (d->format & BAM_PLF_CNS) {
+ for (i = rms_aux = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pu + i;
+ int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+ rms_aux += tmp * tmp;
+ }
+ 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) {
+ int c = pu[i].b->core.qual + 33;
+ if (c > 126) c = 126;
+ putchar(c);
+ }
+ }
+ // print read position
+ if (d->format & BAM_PLF_READPOS) {
+ putchar('\t');
+ for (i = 0; i < n; ++i) {
+ int x = pu[i].qpos;
+ int l = pu[i].b->core.l_qseq;
+ printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(',');
+ }
+ }
+ putchar('\n');
+ // 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, 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\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;
+}
+
+int bam_pileup(int argc, char *argv[])
+{
+ 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->max_depth = 1024; d->tid = -1; d->mask = BAM_DEF_MASK; d->min_baseQ = 13;
+ d->c = bam_maqcns_init();
+ d->c->errmod = BAM_ERRMOD_MAQ2; // change the default model
+ d->ido = bam_maqindel_opt_init();
+ while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PAQ:C:B")) >= 0) {
+ switch (c) {
+ case 'Q': d->c->min_baseQ = atoi(optarg); break;
+ case 'C': d->capQ_thres = atoi(optarg); break;
+ case 'B': d->format |= BAM_PLF_NOBAQ; break;
+ case 'a': d->c->errmod = BAM_ERRMOD_SOAP; break;
+ case 'A': d->c->errmod = BAM_ERRMOD_MAQ; break;
+ case 's': d->format |= BAM_PLF_SIMPLE; break;
+ case 't': fn_list = strdup(optarg); break;
+ case 'l': fn_pos = strdup(optarg); break;
+ case 'f': fn_fa = strdup(optarg); break;
+ 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); d->ido->r_snp = d->c->het_rate; break;
+ case 'M': d->c->cap_mapQ = atoi(optarg); break;
+ case 'd': d->max_depth = 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 'P': d->format |= BAM_PLF_READPOS; 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(pysamerr, "[bam_pileup] unrecognized -R\n");
+ break;
+ default: fprintf(pysamerr, "Unrecognizd option '-%c'.\n", c); return 1;
+ }
+ }
+ if (d->c->errmod != BAM_ERRMOD_MAQ2) d->c->theta += 0.02;
+ if (d->c->theta > 1.0) d->c->theta = 1.0;
+ if (fn_list) is_SAM = 1;
+ if (optind == argc) {
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: samtools pileup [options] <in.bam>|<in.sam>\n\n");
+ fprintf(pysamerr, "Option: -s simple (yet incomplete) pileup format\n");
+ fprintf(pysamerr, " -S the input is in SAM\n");
+ fprintf(pysamerr, " -B disable BAQ computation\n");
+ fprintf(pysamerr, " -A use the original MAQ model for SNP calling (DEPRECATED)\n");
+ fprintf(pysamerr, " -2 output the 2nd best call and quality\n");
+ fprintf(pysamerr, " -i only show lines/consensus with indels\n");
+ fprintf(pysamerr, " -Q INT min base quality (possibly capped by BAQ) [%d]\n", d->c->min_baseQ);
+ fprintf(pysamerr, " -C INT coefficient for adjusting mapQ of poor mappings [%d]\n", d->capQ_thres);
+ fprintf(pysamerr, " -m INT filtering reads with bits in INT [0x%x]\n", d->mask);
+ fprintf(pysamerr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
+ fprintf(pysamerr, " -d INT limit maximum depth for indels [%d]\n", d->max_depth);
+ fprintf(pysamerr, " -t FILE list of reference sequences (force -S)\n");
+ fprintf(pysamerr, " -l FILE list of sites at which pileup is output\n");
+ fprintf(pysamerr, " -f FILE reference sequence in the FASTA format\n\n");
+ fprintf(pysamerr, " -c compute the consensus sequence\n");
+ fprintf(pysamerr, " -v print variants only (for -c)\n");
+ fprintf(pysamerr, " -g output in the GLFv3 format (DEPRECATED)\n");
+ fprintf(pysamerr, " -T FLOAT theta in maq consensus calling model (for -c) [%.4g]\n", d->c->theta);
+ fprintf(pysamerr, " -N INT number of haplotypes in the sample (for -c) [%d]\n", d->c->n_hap);
+ fprintf(pysamerr, " -r FLOAT prior of a difference between two haplotypes (for -c) [%.4g]\n", d->c->het_rate);
+ fprintf(pysamerr, " -G FLOAT prior of an indel between two haplotypes (for -c) [%.4g]\n", d->ido->r_indel);
+ fprintf(pysamerr, " -I INT phred prob. of an indel in sequencing/prep. (for -c) [%d]\n", d->ido->q_indel);
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Warning: Please use the `mpileup' command instead `pileup'. `Pileup' is deprecated!\n\n");
+ 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
+ glf3_header_t *h;
+ h = glf3_header_init();
+ d->fp_glf = bgzf_fdopen(fileno(stdout), "w");
+ glf3_header_write(d->fp_glf, h);
+ glf3_header_destroy(h);
+ }
+ if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
+ fprintf(pysamerr, "[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 = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
+ if (fp == 0 || fp->header == 0) {
+ fprintf(pysamerr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n");
+ return 1;
+ }
+ d->h = fp->header;
+ if (fn_pos) d->hash = load_pos(fn_pos, d->h);
+ { // run pileup
+ extern int bam_prob_realn(bam1_t *b, const char *ref);
+ extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
+ bam1_t *b;
+ int ret, tid, pos, n_plp;
+ bam_plp_t iter;
+ const bam_pileup1_t *plp;
+ b = bam_init1();
+ iter = bam_plp_init(0, 0);
+ bam_plp_set_mask(iter, d->mask);
+ while ((ret = samread(fp, b)) >= 0) {
+ int skip = 0;
+ if ((int)b->core.tid < 0) break;
+ // update d->ref if necessary
+ if (d->fai && (int)b->core.tid != d->tid) {
+ free(d->ref);
+ d->ref = faidx_fetch_seq(d->fai, d->h->target_name[b->core.tid], 0, 0x7fffffff, &d->len);
+ d->tid = b->core.tid;
+ }
+ if (d->ref && (d->format&BAM_PLF_CNS) && !(d->format&BAM_PLF_NOBAQ)) bam_prob_realn(b, d->ref);
+ if (d->ref && (d->format&BAM_PLF_CNS) && d->capQ_thres > 10) {
+ int q = bam_cap_mapQ(b, d->ref, d->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 ((d->format&BAM_PLF_CNS) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
+ if (skip) continue;
+ bam_plp_push(iter, b);
+ while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0)
+ pileup_func(tid, pos, n_plp, plp, d);
+ }
+ bam_plp_push(iter, 0);
+ while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0)
+ pileup_func(tid, pos, n_plp, plp, d);
+ bam_plp_destroy(iter);
+ bam_destroy1(b);
+ }
+ samclose(fp); // d->h will be destroyed here
+ }
+
+ // free
+ if (d->format & BAM_PLF_GLF) bgzf_close(d->fp_glf);
+ if (fn_pos) { // free the hash table
+ khint_t k;
+ for (k = kh_begin(d->hash); k < kh_end(d->hash); ++k)
+ if (kh_exist(d->hash, k)) free(kh_val(d->hash, k));
+ kh_destroy(64, d->hash);
+ }
+ free(fn_pos); free(fn_list); free(fn_fa);
+ if (d->fai) fai_destroy(d->fai);
+ bam_maqcns_destroy(d->c);
+ free(d->ido); free(d->ref); free(d);
+ return 0;
+}
+
+/***********
+ * mpileup *
+ ***********/
+
#include <assert.h>
#include "bam2bcf.h"
#include "sample.h"
#define MPLP_NO_INDEL 0x400
#define MPLP_EXT_BAQ 0x800
#define MPLP_ILLUMINA13 0x1000
-#define MPLP_IGNORE_RG 0x2000
-#define MPLP_PRINT_POS 0x4000
-#define MPLP_PRINT_MAPQ 0x8000
void *bed_read(const char *fn);
void bed_destroy(void *_h);
}
static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
- int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
+ int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp)
{
int i, j;
memset(m->n_plp, 0, m->n * sizeof(int));
const bam_pileup1_t *p = plp[i] + j;
uint8_t *q;
int id = -1;
- q = ignore_rg? 0 : bam_aux_get(p->b, "RG");
+ q = bam_aux_get(p->b, "RG");
if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
if (id < 0 || id >= m->n) {
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, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
+ 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;
data[i]->conf = conf;
h_tmp = bam_header_read(data[i]->fp);
data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
- bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
+ 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;
fprintf(pysamerr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
exit(1);
}
- if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
+ if (i == 0) beg0 = beg, end0 = end;
data[i]->iter = bam_iter_query(idx, tid, beg, end);
bam_index_destroy(idx);
}
bca->min_frac = conf->min_frac;
bca->min_support = conf->min_support;
}
- if (tid0 >= 0 && conf->fai) { // region is set
- ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
- ref_tid = tid0;
- for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
- } else ref_tid = -1, ref = 0;
+ 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)
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
if (tid != ref_tid) {
free(ref); ref = 0;
- if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
+ if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
ref_tid = tid;
}
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, conf->flag & MPLP_IGNORE_RG);
+ 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)
for (i = 0; i < n; ++i) {
int j;
printf("\t%d\t", n_plp[i]);
- if (n_plp[i] == 0) {
- printf("*\t*"); // FIXME: printf() is very slow...
- if (conf->flag & MPLP_PRINT_POS) printf("\t*");
- } else {
+ if (n_plp[i] == 0) printf("*\t*");
+ else {
for (j = 0; j < n_plp[i]; ++j)
pileup_seq(plp[i] + j, pos, ref_len, ref);
putchar('\t');
if (c > 126) c = 126;
putchar(c);
}
- if (conf->flag & MPLP_PRINT_MAPQ) {
- putchar('\t');
- for (j = 0; j < n_plp[i]; ++j) {
- int c = plp[i][j].b->core.qual + 33;
- if (c > 126) c = 126;
- putchar(c);
- }
- }
- if (conf->flag & MPLP_PRINT_POS) {
- putchar('\t');
- for (j = 0; j < n_plp[i]; ++j) {
- if (j > 0) putchar(',');
- printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
- }
- }
}
}
putchar('\n');
int nfiles = 0, use_orphan = 0;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
- #define MPLP_PRINT_POS 0x4000
mplp.max_mq = 60;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
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, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6Os")) >= 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);
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; 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 'R': mplp.flag |= MPLP_IGNORE_RG; break;
- case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
- case 'O': mplp.flag |= MPLP_PRINT_POS; 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;
fprintf(pysamerr, " -A count anomalous read pairs\n");
fprintf(pysamerr, " -B disable BAQ computation\n");
fprintf(pysamerr, " -b FILE list of input BAM files [null]\n");
- fprintf(pysamerr, " -C INT parameter for adjusting mapQ; 0 to disable [0]\n");
fprintf(pysamerr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
fprintf(pysamerr, " -E extended BAQ for higher sensitivity but lower specificity\n");
fprintf(pysamerr, " -f FILE faidx indexed reference sequence file [null]\n");
fprintf(pysamerr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
fprintf(pysamerr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
fprintf(pysamerr, " -r STR region in which pileup is generated [null]\n");
- fprintf(pysamerr, " -R ignore RG tags\n");
fprintf(pysamerr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(pysamerr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
fprintf(pysamerr, "\nOutput options:\n\n");
fprintf(pysamerr, " -D output per-sample DP in BCF (require -g/-u)\n");
fprintf(pysamerr, " -g generate BCF output (genotype likelihoods)\n");
- fprintf(pysamerr, " -O output base positions on reads (disabled by -g/-u)\n");
- fprintf(pysamerr, " -s output mapping quality (disabled by -g/-u)\n");
fprintf(pysamerr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
fprintf(pysamerr, " -u generate uncompress BCF output\n");
fprintf(pysamerr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
projects / pysam.git / blobdiff