* samtools-0.1.5-31 (r448)

 * fixed an issue when the last CIGAR is I or D

diff --git a/ChangeLog b/ChangeLog
index d6a6f3340e1e6d46d96d0f7672d5cc4e5a7659d3..969fb28b058f6423d7dfd30ac72e42aaabcaa2d3 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,231 @@
+------------------------------------------------------------------------
+r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-30 (r447)
+ * fixed a bug in bam_aux_get(): 'A' is not checked
+
+------------------------------------------------------------------------
+r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bamtk.c
+
+ * 
+
+------------------------------------------------------------------------
+r444 | lh3lh3 | 2009-08-11 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_sort.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-28 (r444)
+ * bug in "merge -n"
+
+------------------------------------------------------------------------
+r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-27 (r443)
+ * SEQ and QUAL can be "*"
+ * parse CIGAR "=" and "X" as "M"
+
+------------------------------------------------------------------------
+r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/md5.c
+   M /trunk/samtools/misc/md5.h
+   M /trunk/samtools/misc/md5fa.c
+
+ * samtools-0.1.5-26 (r442)
+ * replace RSA Inc md5.* with ones under permissive lincense
+ * fixed a bug in detecting unsorted bam in pileup
+
+------------------------------------------------------------------------
+r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bgzf.c
+   M /trunk/samtools/bgzf.h
+   M /trunk/samtools/bgzip.c
+
+Change copyright notices now that MIT has approved open source distribution.
+
+------------------------------------------------------------------------
+r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_stat.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-25 (r436)
+ * in flagstats, do not report singletons if both ends are unmapped
+
+------------------------------------------------------------------------
+r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/misc/maq2sam.c
+
+fixed a SERIOUS bug in setting 0x20 flag
+
+------------------------------------------------------------------------
+r438 | lh3lh3 | 2009-08-04 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/misc/samtools.pl
+
+fixed two minor bugs (suggested by Tim M Storm)
+
+------------------------------------------------------------------------
+r437 | lh3lh3 | 2009-08-04 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/samtools.pl
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-24 (r435)
+ * fixed a typo
+
+------------------------------------------------------------------------
+r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-23 (r434)
+ * in tview, press 'r' to show read names rather than sequences
+
+------------------------------------------------------------------------
+r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/knetfile.c
+
+ * tried to fixed the buggy FTP random access in Windows. FAILED.
+ * anyway, MinGW seems to have problem with "%lld".
+
+------------------------------------------------------------------------
+r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/Makefile.mingw
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/faidx.c
+   M /trunk/samtools/razf.c
+   A /trunk/samtools/win32/libcurses.a
+   A /trunk/samtools/win32/xcurses.h
+
+ * samtools-0.1.5-22 (r432)
+ * faidx: fixed compitability issue with _WIN32
+ * razf: fixed potential compitability issue with _WIN32
+ * PDCurses support in Windows
+
+------------------------------------------------------------------------
+r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/win32/libz.a
+
+replace the GnuWin32 version of libz.a with my own build with MinGW.
+
+------------------------------------------------------------------------
+r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/knetfile.c
+
+add comments
+
+------------------------------------------------------------------------
+r429 | lh3lh3 | 2009-08-01 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile.mingw
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/knetfile.c
+   M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.5-21 (r428)
+ * knetfile.c is now compatible with mingw-winsock
+
+------------------------------------------------------------------------
+r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.mingw
+
+simplify MinGW Makefile
+
+------------------------------------------------------------------------
+r427 | lh3lh3 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
+Changed paths:
+   A /trunk/samtools/Makefile.mingw
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   A /trunk/samtools/win32
+   A /trunk/samtools/win32/libz.a
+   A /trunk/samtools/win32/zconf.h
+   A /trunk/samtools/win32/zlib.h
+
+ * samtools-0.1.5-20 (r427)
+ * MinGW support. At least SAM<->BAM conversion is working. Other
+   functionality are not tested at the moment.
+ * zlib headers and Windows version of libz.a are included in win32/
+
+------------------------------------------------------------------------
+r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-19 (r426)
+ * fixed a bug caused by recent modifications. Sorry.
+
+------------------------------------------------------------------------
+r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bgzf.c
+
+compatible with Windows binary files
+
+------------------------------------------------------------------------
+r424 | lh3lh3 | 2009-07-31 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bam_maqcns.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.5-18 (r423)
+ * output additional information in pileup indel lines, for the purepose
+   of debugging at the moment
+ * in tview, optionally allow to treat reference skip as deletion
+
+------------------------------------------------------------------------
+r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/misc/psl2sam.pl
+
+convert BLAT psl to SAM.
+
+------------------------------------------------------------------------
+r422 | lh3lh3 | 2009-07-30 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bgzf.c
+   M /trunk/samtools/bgzf.h
+   M /trunk/samtools/knetfile.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-17 (r422)
+ * fixed a but in knetfile.c when seek type is not SEEK_SET
+ * write an empty BGZF block to every BGZF file
+ * check BGZF EOF marker in bam_header_read()
+ * update ChangeLog
+
 ------------------------------------------------------------------------
 r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
 Changed paths:

diff --git a/bam_pileup.c b/bam_pileup.c
index 983c08e6411623da1e322fd071859be4a0af5c3a..f68f400ab5cd086dc88a33e14899abe6cd4e53bb 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -78,6 +78,10 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
                                                int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
                                                if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
                                                else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
+                                               if (op_next == BAM_CDEL || op_next == BAM_CINS) {
+                                                       if (k + 2 < c->n_cigar) op_next = bam1_cigar(b)[k+2]&BAM_CIGAR_MASK;
+                                                       else p->is_tail = 1;
+                                               }
                                                if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP)
                                                        p->is_tail = 1; // tail
                                        } else p->is_tail = 1; // this is the last operation; set tail

diff --git a/bamtk.c b/bamtk.c
index 7150c78fb879d8125fd02be5528b731edc6d23fa..c6a571463cb608639dd23d71251ad2c70210c649 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-30 (r447)"
+#define PACKAGE_VERSION "0.1.5-31 (r448)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index 412243f9a5485a1962473fe4ce4dd3559a4e3597..01038f1fab67c6585e2788eb19e2ae4a6e015ab2 100755 (executable)
--- a/misc/wgsim_eval.pl
+++ b/misc/wgsim_eval.pl
@@ -30,8 +30,11 @@ sub wgsim_eval {
        $_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
        --$rght;
        # correct for soft clipping
+       my ($left0, $rght0) = ($left, $rght);
        $left -= $1 if (/^(\d+)[SH]/);
        $rght += $1 if (/(\d+)[SH]$/);
+       $left0 -= $1 if (/(\d+)[SH]$/);
+       $rght0 += $1 if (/^(\d+)[SH]/);
        # skip unmapped reads
        next if (($t[1]&0x4) || $chr eq '*');
        # parse read name and check
@@ -41,19 +44,19 @@ sub wgsim_eval {
          } else {
                if ($flag & 2) {
                  if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
-                       $is_correct = 0 if (abs($2 - $left) > $gap);
+                       $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
                  } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
-                       $is_correct = 0 if (abs($3 - $rght) > $gap);
+                       $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap);
                  } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
-                       $is_correct = 0 if (abs($3 - $left) > $gap);
+                       $is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);
                  } else { # R3, reverse
-                       $is_correct = 0 if (abs($2 - $rght) > $gap);
+                       $is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);
                  }
                } else {
                  if ($t[1] & 0x10) { # reverse
-                       $is_correct = 0 if (abs($3 - $rght) > $gap); # in case of indels that are close to the end of a reads
+                       $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap); # in case of indels that are close to the end of a reads
                  } else {
-                       $is_correct = 0 if (abs($2 - $left) > $gap);
+                       $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
                  }
                }
          }