From: Heng Li <lh3@live.co.uk>
Date: Wed, 8 Apr 2009 14:15:05 +0000 (+0000)
Subject:  * samtools-0.1.2-21
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c8044e25522a63130998db47cb43787336fdc062;p=samtools.git

 * samtools-0.1.2-21
 * fixed a nasty bug in `fixmate'
---

diff --git a/bam_mate.c b/bam_mate.c
index f37f8f8..61f808a 100644
--- a/bam_mate.c
+++ b/bam_mate.c
@@ -29,9 +29,9 @@ void bam_mating_core(bamFile in, bamFile out)
 					pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
 					cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
 				} else cur->core.isize = pre->core.isize = 0;
-				if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FREVERSE;
+				if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
 				else cur->core.flag &= ~BAM_FMREVERSE;
-				if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FREVERSE;
+				if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
 				else pre->core.flag &= ~BAM_FMREVERSE;
 				if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
 				if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
diff --git a/bamtk.c b/bamtk.c
index aeb7d0a..95c206f 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-20"
+#define PACKAGE_VERSION "0.1.2-21"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/misc/soap2sam.pl b/misc/soap2sam.pl
index 1628c0f..b37135e 100755
--- a/misc/soap2sam.pl
+++ b/misc/soap2sam.pl
@@ -64,6 +64,8 @@ sub soap2sam_aux {
   my @t = split(/\s+/, $line);
   return -1 if (@t < 9 || $line =~ /^\s/ || !$t[0]);
   @$s = ();
+  # fix SOAP-2.1.x bugs
+  @t = @t[0..2,4..$#t] unless ($t[3] =~ /^\d+$/);
   # read name
   $s->[0] = $t[0];
   $s->[0] =~ s/\/[12]$//g;