* prepare to replace kaln with kprobaln in realignment

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index b43a015c6e62adf0e9faf1341aec62a08b3c7040..7f6e288014cf1e0b627f3e7f2150e6dfbef5a03d 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -5,6 +5,7 @@
 #include "bam2bcf.h"
 #include "ksort.h"
 #include "kaln.h"
+#include "kprobaln.h"
 #include "khash.h"
 KHASH_SET_INIT_STR(rg)
 
@@ -274,9 +275,17 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                for (l = qbeg; l < qend; ++l)
                                        query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
                                // do alignment; this takes most of computing time for indel calling
-                               sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
-                                                                        (uint8_t*)query, qend - qbeg, &ap);
-                               score[K*n_types + t] = -sc;
+                               if (0) {
+                                       uint8_t *qq = calloc(qend - qbeg, 1);
+                                       for (l = 0; l < qend - qbeg; ++l) qq[l] = 23;
+                                       sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+                                                                       (uint8_t*)query, qend - qbeg, qq, &kpa_par_alt, 0, 0);
+                                       score[K*n_types + t] = sc;
+                               } else {
+                                       sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+                                                                                (uint8_t*)query, qend - qbeg, &ap);
+                                       score[K*n_types + t] = -sc;
+                               }
 /*
                                for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
                                        fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);