From: Heng Li <lh3@live.co.uk>
Date: Thu, 11 Nov 2010 06:22:59 +0000 (+0000)
Subject:  * samtools-0.1.9-10 (r816)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=b79e085714e6c1dfdcbc3c15fd70ffb2b6c9c70f;p=samtools.git

 * samtools-0.1.9-10 (r816)

 * I know why the forward method fails. it is because of zero base
   qualities. when that is fixed, the forward method seems to give
   better results than Viterbi, as it should be. I am tired...
---

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 2e0b04d..7713b51 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -277,7 +277,7 @@ 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 is the bottleneck
-				if (0) {
+				if (1) {
 					const uint8_t *qual = bam1_qual(p->b), *bq;
 					uint8_t *qq = 0;
 					qq = calloc(qend - qbeg, 1);
@@ -286,12 +286,13 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 					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;
 					free(qq);
-				} else {
+				} 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;
diff --git a/bamtk.c b/bamtk.c
index 922dee3..09d64ad 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.9-9 (r810)"
+#define PACKAGE_VERSION "0.1.9-10 (r816)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);