* samtools-0.1.3-19 (r275)

 * a minor change to the bam1_t struct: added back "void *hash" for the
   backward compatibility with Bio::DB::Sam

diff --git a/ChangeLog b/ChangeLog
index a096816027cd67abdd8d8e139ea0ead703203186..cbe3178766f0cd4204fc125174082b2b95708cbf 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,197 @@
+------------------------------------------------------------------------
+r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_rmdupse.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-18 (r273)
+ * rmdupse: do not remove unmapped reads
+
+------------------------------------------------------------------------
+r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_rmdupse.c
+
+change a parameter. It does nothing
+
+------------------------------------------------------------------------
+r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile.am
+   M /trunk/samtools/Makefile.generic
+   M /trunk/samtools/Makefile.lite
+   A /trunk/samtools/bam_rmdupse.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/configure.ac
+
+ * samtools-0.1.3-17 (r271)
+ * added 'rmdupse' command
+
+------------------------------------------------------------------------
+r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-16 (r267)
+ * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
+
+------------------------------------------------------------------------
+r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-15 (r266)
+ * report an error if a non-* reference is present while @SQ is absent
+
+------------------------------------------------------------------------
+r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-14 (r262)
+ * make samopen() recognize @SQ header lines
+
+------------------------------------------------------------------------
+r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bgzf.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-13 (r260)
+ * report error for file I/O error
+
+------------------------------------------------------------------------
+r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.am
+
+update Makefile.am
+
+------------------------------------------------------------------------
+r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam.h
+
+ * samtools-0.1.3-12 (r259)
+ * use the new I/O interface in pileup
+
+------------------------------------------------------------------------
+r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile.generic
+   M /trunk/samtools/Makefile.lite
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   A /trunk/samtools/sam.c
+   A /trunk/samtools/sam.h
+   A /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-11 (r258)
+ * unify the interface to BAM and SAM I/O
+
+------------------------------------------------------------------------
+r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile.lite
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-10 (r257)
+ * allow hex with "pileup -m"
+
+------------------------------------------------------------------------
+r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_lpileup.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-9 (r256)
+ * fixed a bug in bam_lpileup.c
+ * I do not know if this also fixes the bug causing assertion failure in the tview
+
+------------------------------------------------------------------------
+r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-8 (r251)
+ * fixed a bug when there are reads without coordinates
+
+------------------------------------------------------------------------
+r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/AUTHORS
+   A /trunk/samtools/README
+   M /trunk/samtools/cleanup.sh
+
+added missing files
+
+------------------------------------------------------------------------
+r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.generic
+   M /trunk/samtools/Makefile.lite
+   M /trunk/samtools/configure.ac
+   M /trunk/samtools/misc/Makefile.generic
+
+improve large file support in compilation
+
+------------------------------------------------------------------------
+r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/INSTALL
+
+update INSTALL
+
+------------------------------------------------------------------------
+r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.am
+   M /trunk/samtools/autogen.sh
+   M /trunk/samtools/cleanup.sh
+   M /trunk/samtools/configure.ac
+   A /trunk/samtools/misc/Makefile.am
+
+fixed various issues about the GNU building scripts
+
+------------------------------------------------------------------------
+r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   D /trunk/samtools/Makefile
+   A /trunk/samtools/Makefile.am
+   A /trunk/samtools/Makefile.generic
+   A /trunk/samtools/autogen.sh
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+   A /trunk/samtools/cleanup.sh
+   A /trunk/samtools/configure.ac
+   D /trunk/samtools/misc/Makefile
+   A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
+
+ * samtools-0.1.3-7 (r246)
+ * incorporated revisions from Nils Homer
+ * enhanced support of displaying color-space reads
+
 ------------------------------------------------------------------------
 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
 Changed paths:

diff --git a/bam.h b/bam.h
index 163dc893e192d6eaa9ebfcc3b3b8614d142ca211..a784a1f3f7f919d38e771a38a1a2d7b5d35cde2e 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -190,6 +190,7 @@ typedef struct {
        bam1_core_t core;
        int l_aux, data_len, m_data;
        uint8_t *data;
+       void *hash; // for backward compatibility. It is NEVER used.
 } bam1_t;
 
 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)

diff --git a/bamtk.c b/bamtk.c
index 2b005a5cb116c128c2f33c64ac3d8d012cbcb68c..9bb236bf7de20749fc128db8e19152a4925cb7e9 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-18 (r273)"
+#define PACKAGE_VERSION "0.1.3-19 (r275)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);