* samtools-0.1.9-2 (r797)

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 1e8a2044305c4449713731fe95787b5105635d8e..25e2a86a72958ff19aa41e88b6b003816678029c 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -1,4 +1,5 @@
 #include <assert.h>
+#include <ctype.h>
 #include "bam.h"
 #include "bam2bcf.h"
 #include "ksort.h"
@@ -44,6 +45,19 @@ static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
        return q < qh? q : qh;
 }
 
+static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
+{
+       int i, j, max = 0, max_i = pos, score = 0;
+       l = abs(l);
+       for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
+               if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
+               else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
+               if (score < 0) break;
+               if (max < score) max = score, max_i = i;
+       }
+       return max_i - pos;
+}
+
 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref)
 {
        extern void ks_introsort_uint32_t(int, uint32_t*);
@@ -149,10 +163,17 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
        ref2  = calloc(right - left + max_ins + 2, 1);
        query = calloc(right - left + max_rd_len + max_ins + 2, 1);
        score = calloc(N * n_types, sizeof(int));
+       bca->indelreg = 0;
        for (t = 0; t < n_types; ++t) {
-               int l;
+               int l, ir;
                ka_param2_t ap = ka_param2_qual;
                ap.band_width = abs(types[t]) + 3;
+               // compute indelreg
+               if (types[t] == 0) ir = 0;
+               else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
+               else ir = est_indelreg(pos, ref, -types[t], 0);
+               if (ir > bca->indelreg) bca->indelreg = ir;
+//             fprintf(stderr, "%d, %d, %d\n", pos, types[t], ir);
                // write ref2
                for (k = 0, j = left; j <= pos; ++j)
                        ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
@@ -233,7 +254,9 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 //                             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);
                        }
                }
-               // determine bca->indel_types[]
+               // determine bca->indel_types[] and bca->inscns
+               bca->maxins = max_ins;
+               bca->inscns = realloc(bca->inscns, bca->maxins * 4);
                for (t = 0; t < n_types; ++t)
                        sumq[t] = sumq[t]<<6 | t;
                for (t = 1; t < n_types; ++t) // insertion sort
@@ -247,8 +270,10 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                        sumq[0] = tmp;
                }
                for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
-               for (t = 0; t < 4 && t < n_types; ++t)
+               for (t = 0; t < 4 && t < n_types; ++t) {
                        bca->indel_types[t] = types[sumq[t]&0x3f];
+                       memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
+               }
                // update p->aux
                for (s = K = 0; s < n; ++s) {
                        for (i = 0; i < n_plp[s]; ++i, ++K) {
@@ -261,7 +286,6 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                        }
                }               
        }
-       // FIXME: to set the inserted sequence
        free(score);
        // free
        free(types); free(inscns);