* samtools-0.1.9-r823

 * the BQ tag is now 64 shifted, not 33 shifted

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 7ce6cd4294d8f0e2a83b78c3e0f7ac0d86e5602a..518768d4af3095d4ad178539acae0cbb0ed736bb 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -289,7 +289,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                        bq = (uint8_t*)bam_aux_get(p->b, "BQ");
                                        if (bq) ++bq; // skip type
                                        for (l = qbeg; l < qend; ++l) {
-                                               qq[l - qbeg] = bq? qual[l] + (bq[l] - 33) : qual[l];
+                                               qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];
                                                if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
                                                if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
                                        }

diff --git a/bam_md.c b/bam_md.c
index 47ec97c124b3fae015bb126b3d99c936308daa00..29b315f4e9235f4e83516d6fb544821185d19a82 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -220,7 +220,7 @@ int bam_prob_realn_core(bam1_t *b, const char *ref, int write_bq)
                        else if (op == BAM_CDEL) x += l;
                }
                if (write_bq) {
-                       for (i = 0; i < c->l_qseq; ++i) bq[i] = bq[i] - qual[i] + 33;
+                       for (i = 0; i < c->l_qseq; ++i) bq[i] = bq[i] - qual[i] + 64;
                        bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq);
                        free(bq);
                }

diff --git a/bamtk.c b/bamtk.c
index cb7b8a0cf6c20743a6a96c1fb1117d5d60ae210d..ef11b06a7366db2a2f1f0088d46824d894fed8a6 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.9-16 (r822)"
+#define PACKAGE_VERSION "0.1.9-16 (r823)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);