* samtools-0.1.2-21

 * fixed a nasty bug in `fixmate'

diff --git a/bam_mate.c b/bam_mate.c
index f37f8f836b04b499cfeae8dc616e992bfe2c6310..61f808a26402e9bd1d332f40074b4b3ca1f89dd3 100644 (file)
--- 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 aeb7d0a77ecca4a0faef75eff8c559f87ff06cb3..95c206f381f090dcae39ee8afd25b85c44e4f34b 100644 (file)
--- 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 1628c0f2230b4cfbb45f3830e1e93bc2cb097e94..b37135e811c6300d734488ae5a112f421bb920b5 100755 (executable)
--- 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;