From f6a84f5598383371a6cd5b3f82be3f8c3419aa6a Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Tue, 12 May 2009 13:28:39 +0000
Subject: [PATCH]  * samtools-0.1.3-18 (r273)  * rmdupse: do not remove
 unmapped reads

---
 bam_rmdupse.c | 3 ++-
 bamtk.c       | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/bam_rmdupse.c b/bam_rmdupse.c
index 272fa99..df03717 100644
--- a/bam_rmdupse.c
+++ b/bam_rmdupse.c
@@ -63,12 +63,13 @@ static int fill_buf(samfile_t *in, buffer_t *buf)
 		for (i = 0; i < c->l_qseq; ++i) e->score += qual[i] + 1;
 		e->score = (double)e->score / sqrt(c->l_qseq + 1);
 		is_mapped = (c->tid < 0 || c->tid >= in->header->n_targets || (c->flag&BAM_FUNMAP))? 0 : 1;
+		if (!is_mapped) e->score = -1;
 		if (is_mapped && (c->flag & BAM_FREVERSE)) {
 			e->rpos = b->core.pos + bam_calend(&b->core, bam1_cigar(b));
 			if (min_rpos > e->rpos) min_rpos = e->rpos;
 		}
 		if (buf->n >= capacity) {
-			if (c->pos <= min_rpos) capacity += BLOCK_SIZE;
+			if (is_mapped && c->pos <= min_rpos) capacity += BLOCK_SIZE;
 			else break;
 		}
 	}
diff --git a/bamtk.c b/bamtk.c
index 6f030a6..2b005a5 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-17 (r271)"
+#define PACKAGE_VERSION "0.1.3-18 (r273)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
-- 
2.39.5