Imported Upstream version 0.6

[pysam.git] / samtools / bam2bcf_indel.c.pysam.c

diff --git a/samtools/bam2bcf_indel.c.pysam.c b/samtools/bam2bcf_indel.c.pysam.c
index b72864845374b07be7d9c0fb1ffb3ecd4c91b7cb..cf86ca3e39f6aad8c222ed8048fcc56f78fff62c 100644 (file)
--- a/samtools/bam2bcf_indel.c.pysam.c
+++ b/samtools/bam2bcf_indel.c.pysam.c
@@ -5,12 +5,14 @@
 #include <string.h>
 #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
 
@@ -66,7 +68,7 @@ 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;
@@ -112,7 +114,6 @@ 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;
@@ -169,6 +170,12 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
                        free(aux); return -1;
                }
+               if (n_types >= 64) {
+                       free(aux);
+                       if (bam_verbose >= 2) 
+                               fprintf(pysamerr, "[%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;
                types[t++] = aux[0] - MINUS_CONST; 
@@ -179,7 +186,6 @@ 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;
@@ -218,7 +224,7 @@ 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;