From 53fb97c63563f75dfa831433f6cb639c0c269475 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 12 May 2009 20:14:10 +0000 Subject: [PATCH] * 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 --- ChangeLog | 194 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ bam.h | 1 + bamtk.c | 2 +- 3 files changed, 196 insertions(+), 1 deletion(-) diff --git a/ChangeLog b/ChangeLog index a096816..cbe3178 100644 --- 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 163dc89..a784a1f 100644 --- 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 2b005a5..9bb236b 100644 --- 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[]); -- 2.39.5