X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf_indel.c;h=9aea5f9d669f79850fb45438fdcf1183c3e1227f;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=c157bc65b9663d62f3ede6863d55d0fe26e7e152;hpb=d1643d6e5e6ec3a7cb1ef8b62b9a6f9b21ff2527;p=samtools.git diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c index c157bc6..9aea5f9 100644 --- a/bam2bcf_indel.c +++ b/bam2bcf_indel.c @@ -3,12 +3,14 @@ #include #include "bam.h" #include "bam2bcf.h" -#include "ksort.h" #include "kaln.h" #include "kprobaln.h" #include "khash.h" KHASH_SET_INIT_STR(rg) +#include "ksort.h" +KSORT_INIT_GENERIC(uint32_t) + #define MINUS_CONST 0x10000000 #define INDEL_WINDOW_SIZE 50 @@ -64,7 +66,7 @@ static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, for (k = 0; k < c->n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int l = cigar[k] >> BAM_CIGAR_SHIFT; - if (op == BAM_CMATCH) { + if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (c->pos > tpos) return y; if (x + l > tpos) { *_tpos = tpos; @@ -110,7 +112,6 @@ static inline int est_indelreg(int pos, const char *ref, int l, char *ins4) int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, const void *rghash) { - extern void ks_introsort_uint32_t(int, uint32_t*); int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2; int N, K, l_run, ref_type, n_alt; char *inscns = 0, *ref2, *query, **ref_sample; @@ -141,31 +142,53 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla if (s == n) return -1; // there is no indel at this position. for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads { // find out how many types of indels are present - int m, n_alt = 0, n_tot = 0; + bca->max_support = bca->max_frac = 0; + int m, n_alt = 0, n_tot = 0, indel_support_ok = 0; uint32_t *aux; aux = calloc(N + 1, 4); m = max_rd_len = 0; aux[m++] = MINUS_CONST; // zero indel is always a type for (s = 0; s < n; ++s) { + int na = 0, nt = 0; for (i = 0; i < n_plp[s]; ++i) { const bam_pileup1_t *p = plp[s] + i; if (rghash == 0 || p->aux == 0) { - ++n_tot; + ++nt; if (p->indel != 0) { - ++n_alt; + ++na; aux[m++] = MINUS_CONST + p->indel; } } j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b)); if (j > max_rd_len) max_rd_len = j; } + float frac = (float)na/nt; + if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac ) + indel_support_ok = 1; + if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac; + n_alt += na; + n_tot += nt; } + // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases), + // check the number of N's in the sequence and skip places where half or more reference bases are Ns. + int nN=0; for (i=pos; i-posi ) { free(aux); return -1; } + ks_introsort(uint32_t, m, aux); // squeeze out identical types for (i = 1, n_types = 1; i < m; ++i) if (aux[i] != aux[i-1]) ++n_types; - if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip - free(aux); return -1; + // Taking totals makes it hard to call rare indels + if ( !bca->per_sample_flt ) + indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1; + if ( n_types == 1 || !indel_support_ok ) { // then skip + free(aux); return -1; + } + if (n_types >= 64) { + free(aux); + if (bam_verbose >= 2) + fprintf(stderr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1); + return -1; } types = (int*)calloc(n_types, sizeof(int)); t = 0; @@ -177,7 +200,6 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla for (t = 0; t < n_types; ++t) if (types[t] == 0) break; ref_type = t; // the index of the reference type (0) - assert(n_types < 64); } { // calculate left and right boundary left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0; @@ -216,7 +238,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k]&0xf; int j, l = cigar[k]>>4; - if (op == BAM_CMATCH) { + if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < l; ++j) if (x + j >= left && x + j < right) cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000; @@ -420,9 +442,11 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499); // pick the smaller between indelQ1 and indelQ2 indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2; + if (indelQ > 255) indelQ = 255; + if (seqQ > 255) seqQ = 255; p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ; -// fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ); +// fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ); } } // determine bca->indel_types[] and bca->inscns