* samtools-r818

 * for indel calling, do two rounds of probabilistic realignments

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 5f4d893a821fd83f3b65a55203d30d771541caaf..ad13eb3774162ad28e6eb9ed29a416e5b191920f 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -113,7 +113,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                          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, *score, N, K, l_run, ref_type, n_alt;
+       int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2;
+       int N, K, l_run, ref_type, n_alt;
        char *inscns = 0, *ref2, *query;
        khash_t(rg) *hash = (khash_t(rg)*)rghash;
        if (ref == 0 || bca == 0) return -1;
@@ -238,13 +239,13 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
        // compute the likelihood given each type of indel for each read
        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));
+       score1 = calloc(N * n_types, sizeof(int));
+       score2 = calloc(N * n_types, sizeof(int));
        bca->indelreg = 0;
        for (t = 0; t < n_types; ++t) {
                int l, ir;
-               kpa_par_t apf = { 1e-4, 1e-2, 10 };
-               ka_param2_t apv = ka_param2_qual;
-               apf.bw = apv.band_width = abs(types[t]) + 3;
+               kpa_par_t apf1 = { 1e-4, 1e-2, 10 }, apf2 = { 1e-6, 1e-3, 10 };
+               apf1.bw = apf2.bw = 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]);
@@ -282,26 +283,26 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                // write the query sequence
                                for (l = qbeg; l < qend; ++l)
                                        query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
-                               // do alignment; this is the bottleneck
-                               if (1) {
+                               { // do realignment; this is the bottleneck
                                        const uint8_t *qual = bam1_qual(p->b), *bq;
-                                       uint8_t *qq = 0;
+                                       uint8_t *qq;
                                        qq = calloc(qend - qbeg, 1);
                                        bq = (uint8_t*)bam_aux_get(p->b, "BQ");
-                                       if (bq) ++bq;
+                                       if (bq) ++bq; // skip type
                                        for (l = qbeg; l < qend; ++l) {
                                                qq[l - qbeg] = bq? qual[l] + (bq[l] - 33) : qual[l];
                                                if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
                                                if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
                                        }
                                        sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
-                                                                       (uint8_t*)query, qend - qbeg, qq, &apf, 0, 0);
-                                       score[K*n_types + t] = sc;
+                                                                       (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0);
+                                       score1[K*n_types + t] = score2[K*n_types + t] = sc;
+                                       if (sc > 5) { // I do not know why, but a long exact match always has sc==5
+                                               sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+                                                                               (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0);
+                                               score2[K*n_types + t] = sc;
+                                       }
                                        free(qq);
-                               } else { // the following block is for testing only
-                                       sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
-                                                                                (uint8_t*)query, qend - qbeg, &apv);
-                                       score[K*n_types + t] = -sc;
                                }
 /*
                                for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
@@ -323,7 +324,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                for (s = K = 0; s < n; ++s) {
                        for (i = 0; i < n_plp[s]; ++i, ++K) {
                                bam_pileup1_t *p = plp[s] + i;
-                               int *sct = &score[K*n_types], indelQ, seqQ;
+                               int *sct = &score1[K*n_types], indelQ1, indelQ2, seqQ, indelQ;
                                for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
                                for (t = 1; t < n_types; ++t) // insertion sort
                                        for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
@@ -335,14 +336,27 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                 * compromise for multi-allelic indels.
                                 */
                                if ((sc[0]&0x3f) == ref_type) {
-                                       indelQ = (sc[1]>>6) - (sc[0]>>6);
+                                       indelQ1 = (sc[1]>>6) - (sc[0]>>6);
                                        seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
                                } else {
                                        for (t = 0; t < n_types; ++t) // look for the reference type
                                                if ((sc[t]&0x3f) == ref_type) break;
-                                       indelQ = (sc[t]>>6) - (sc[0]>>6);
+                                       indelQ1 = (sc[t]>>6) - (sc[0]>>6);
                                        seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
                                }
+                               sct = &score2[K*n_types];
+                               for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+                               for (t = 1; t < n_types; ++t) // insertion sort
+                                       for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+                                               tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+                               if ((sc[0]&0x3f) == ref_type) {
+                                       indelQ2 = (sc[1]>>6) - (sc[0]>>6);
+                               } else {
+                                       for (t = 0; t < n_types; ++t) // look for the reference type
+                                               if ((sc[t]&0x3f) == ref_type) break;
+                                       indelQ2 = (sc[t]>>6) - (sc[0]>>6);
+                               }
+                               indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
                                if (sc[0]>>6 > MAX_SCORE) indelQ = 0; // too many mismatches; something bad possibly happened
                                p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ;
                                sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
@@ -382,7 +396,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                        }
                }               
        }
-       free(score);
+       free(score1); free(score2);
        // free
        free(types); free(inscns);
        return n_alt > 0? 0 : -1;

diff --git a/bamtk.c b/bamtk.c
index da29ed7ac5add7b6e95110778bb66032f34344d1..428e9ed94e491199205e231e74d290f9e941ec3e 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.9-11 (r817)"
+#define PACKAGE_VERSION "0.1.9-12 (r818)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);