From: Heng Li <lh3@live.co.uk>
Date: Mon, 2 Feb 2009 10:12:15 +0000 (+0000)
Subject:  * samtools-0.1.2-3
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c7387993bba745f3cbcff7c400583d68771a2572;p=samtools.git

 * samtools-0.1.2-3
 * fixed a bug in generating GLFv2 for indels
 * improve flagstat report a little bit
---

diff --git a/ChangeLog b/ChangeLog
index 1d47eac..31ec757 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,23 @@
+------------------------------------------------------------------------
+r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   A /trunk/samtools/bam_stat.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-1
+ * added flagstat command
+
+------------------------------------------------------------------------
+r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+
+Release SAMtools-0.1.2
+
 ------------------------------------------------------------------------
 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
 Changed paths:
diff --git a/bam_plcmd.c b/bam_plcmd.c
index dbfc295..58e2be1 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -87,13 +87,12 @@ static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
 		min = g3;
 		if (min > r->gl[0]) min = r->gl[0];
 		if (min > r->gl[1]) min = r->gl[1];
-		g3 -= min;
 		g2.ref_base = 0;
 		g2.type = GLF_TYPE_INDEL;
 		memset(g2.lk, 0, 10);
-		g2.lk[0] = r->gl[0] < 255? r->gl[0] : 255;
-		g2.lk[1] = r->gl[1] < 255? r->gl[1] : 255;
-		g2.lk[2] = g3 < 255? g3 : 255;
+		g2.lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
+		g2.lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
+		g2.lk[2] = g3 - min < 255? g3 - min : 255;
 		*(int16_t*)(g2.lk + 3) = (int16_t)r->indel1;
 		*(int16_t*)(g2.lk + 5) = (int16_t)r->indel2;
 		g2.min_lk = min < 255? min : 255;
diff --git a/bam_stat.c b/bam_stat.c
index 3f58686..1429336 100644
--- a/bam_stat.c
+++ b/bam_stat.c
@@ -58,14 +58,15 @@ int bam_flagstat(int argc, char *argv[])
 	printf("%lld in total\n", s->n_reads);
 	printf("%lld QC failure\n", s->n_qcfail);
 	printf("%lld duplicates\n", s->n_dup);
-	printf("%lld mapped\n", s->n_mapped);
+	printf("%lld mapped (%.2f%%)\n", s->n_mapped, (float)s->n_mapped / s->n_reads * 100.0);
 	printf("%lld paired in sequencing\n", s->n_pair_all);
 	printf("%lld read1\n", s->n_read1);
 	printf("%lld read2\n", s->n_read2);
-	printf("%lld properly paired\n", s->n_pair_good);
-	printf("%lld with both itself and its mate mapped\n", s->n_pair_map);
-	printf("%lld singletons\n", s->n_sgltn);
-	printf("%lld with its mate mapped to a different chr\n", s->n_diffchr);
+	printf("%lld properly paired (%.2f%%)\n", s->n_pair_good, (float)s->n_pair_good / s->n_reads * 100.0);
+	printf("%lld with itself and mate mapped\n", s->n_pair_map);
+	printf("%lld singletons (%.2f%%)\n", s->n_sgltn, (float)s->n_sgltn / s->n_reads * 100.0);
+	printf("%lld with mate mapped to a different chr\n", s->n_diffchr);
+	printf("%lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh);
 	free(s);
 	bam_header_destroy(header);
 	bam_close(fp);
diff --git a/bamtk.c b/bamtk.c
index 0e73016..631502c 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-1"
+#define PACKAGE_VERSION "0.1.2-3"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);