------------------------------------------------------------------------
-r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
+r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_lpileup.c
- M /branches/dev/samtools/bamtk.c
+ A /trunk/samtools/misc/indel_filter.pl
- * samtools-0.1.1-18
- * fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized
+Script for filtering indel results
------------------------------------------------------------------------
-r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
+r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
Changed paths:
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bamtk.c
+ A /trunk/samtools/misc/zoom2sam.pl
- * samtools-0.1.1-17
- * fixed a bug when there are reads without coordinates
- * also recognize type 'c' as 'A'
- * found a bug in bam_lpileup.c; NOT fixed yet
+convert ZOOM to SAM
------------------------------------------------------------------------
-r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
+r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
Changed paths:
- A /branches/dev/samtools/INSTALL
+ A /trunk/samtools/misc/novo2sam.pl
-Instruction for compilation
+add a script to convert novo alignment to SAM
------------------------------------------------------------------------
-r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
+r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
Changed paths:
- M /branches/dev/samtools/Makefile
- A /branches/dev/samtools/Makefile.lite
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/faidx.c
- M /branches/dev/samtools/misc/Makefile
- M /branches/dev/samtools/razf.c
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/ChangeLog.old
+ M /trunk/samtools/samtools.1
- * replaced HAVE_RAZF with _NO_RAZF
- * added Makefile.lite for people who have trouble with razf.c
+update documentation and ChangeLog
------------------------------------------------------------------------
-r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
+r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
Changed paths:
- M /branches/dev/samtools/bam_mate.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/misc/wgsim.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
- * samtools-0.1.1-15
- * fixed another bug in fixmate: unmapped pair has non-zero isize
+ * samtools-0.1.1-19
+ * fixed a bug in "merge" command line
------------------------------------------------------------------------
-r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
+r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
- M /branches/dev/samtools/ChangeLog
- M /branches/dev/samtools/bam_mate.c
- M /branches/dev/samtools/bamtk.c
+ M /trunk/samtools/misc/Makefile
+ A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
+ M /trunk/samtools/misc/export2sam.pl
+ A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
+ A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
+ A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
- * samtools-0.1.1-14
- * fixed a bug in fixmate: isize not equal to zero if two ends mapped to
- different chr
+ * merge from branches/dev/
+ * all future development will happen here
------------------------------------------------------------------------
-r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
+r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bamtk.c
+ M /trunk/samtools/COPYING
+ M /trunk/samtools/ChangeLog
+ A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_lpileup.c
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/examples/00README.txt
+ A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
+ D /trunk/samtools/examples/ex1.fa.fai
+ M /trunk/samtools/examples/ex1.sam.gz
+ M /trunk/samtools/faidx.c
+ A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
+ M /trunk/samtools/glf.h
+ M /trunk/samtools/misc/Makefile
+ M /trunk/samtools/misc/maq2sam.c
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/source.dot
- * samtools-0.1.1-13
- * fixed the prior for hom indels (Richard pointed this out)
+ * Merge from branches/dev/
+ * all future development will happen here at trunk/
------------------------------------------------------------------------
-r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
+r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
Changed paths:
- M /branches/dev/samtools/COPYING
- M /branches/dev/samtools/bam_sort.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/source.dot
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_tview.c
- * samtools-0.1.1-12
- * fixed a bug in sort
- * update source file graph and copyright information
+Fix problem with compiling without curses.
------------------------------------------------------------------------
-r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
+r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
- M /branches/dev/samtools/glf.c
-
-fixed a typo
-
-------------------------------------------------------------------------
-r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
-Changed paths:
- M /branches/dev/samtools/glf.c
-
-added a main function for glf.c
-
-------------------------------------------------------------------------
-r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/bgzf.h
- A /branches/dev/samtools/glf.c
- M /branches/dev/samtools/glf.h
-
- * samtools-0.1.1-11
- * generate binary GLFv2
- * added glfview command to dump GLFv2 binary file
-
-------------------------------------------------------------------------
-r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam_rmdup.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/glf.h
-
- * samtools-0.1.1-10
- * fixed several bugs in rmdup
- * prepare to generate GLF2
-
-------------------------------------------------------------------------
-r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_import.c
- A /branches/dev/samtools/bam_rmdup.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-9
- * implemented rmdup; NOT tested yet
-
-------------------------------------------------------------------------
-r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
-Changed paths:
- M /branches/dev/samtools/examples/00README.txt
-
-update README for typos
-
-------------------------------------------------------------------------
-r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
-Changed paths:
- M /branches/dev/samtools/examples/ex1.sam.gz
-
-update example
-
-------------------------------------------------------------------------
-r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam.c
- A /branches/dev/samtools/bam_mate.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-8
- * added fixmate command
-
-------------------------------------------------------------------------
-r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-7
- * change the reported indel position to the previous way
-
-------------------------------------------------------------------------
-r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-6
- * addd glt output
- * allow to change indel calling parameters at the command line
-
-------------------------------------------------------------------------
-r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_pileup.c
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-5
- * added two more flags
- * allowed to select reads shown in pileup with a mask
-
-------------------------------------------------------------------------
-r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-4
- * fixed a bug in indexing (linear index)
- * prepare to add glt output from pileup
-
-------------------------------------------------------------------------
-r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-3
- * fixed a bug in outputing the coordinate of an indel
-
-------------------------------------------------------------------------
-r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-2
- * pileup: allows to output indel sites only
-
-------------------------------------------------------------------------
-r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bam_maqcns.h
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.1-1
- * implemented a Bayesian indel caller
-
-------------------------------------------------------------------------
-r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
-Changed paths:
- M /branches/dev/samtools/examples/00README.txt
- D /branches/dev/samtools/examples/ex1.fa.fai
-
-Let users generate ex1.fa.fai.
-
-------------------------------------------------------------------------
-r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/bowtie2sam.pl
-
-make the bowtie converter works for "-k 2"
-
-------------------------------------------------------------------------
-r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/export2sam.pl
-
-fixed a bug for "QC" reads
-
-------------------------------------------------------------------------
-r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
-Changed paths:
- A /branches/dev/samtools/misc/bowtie2sam.pl
- M /branches/dev/samtools/misc/soap2sam.pl
-
- * soap2sam.pl: added NM tag
- * bowtie2sam.pl: converter for bowtie
-
-------------------------------------------------------------------------
-r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/misc/soap2sam.pl
-
-soap2sam.pl: convert soap output to SAM
-
-------------------------------------------------------------------------
-r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/misc/wgsim_eval.pl
-
- * wgsim_eval.pl-0.1.1
- * fixed a bug for a contig name like "NT_012345"
-
-------------------------------------------------------------------------
-r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/misc/wgsim_eval.pl
-
- * evaluate alignment for reads generated by wgsim
-
-------------------------------------------------------------------------
-r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/Makefile
- M /branches/dev/samtools/misc/wgsim.c
-
-fixed compiling warnings for wgsim
-
-------------------------------------------------------------------------
-r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/bam_tview.c
-
-remove an unused variable (a compiler warning only)
-
-------------------------------------------------------------------------
-r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/Makefile
- A /branches/dev/samtools/misc/wgsim.c
-
-wgsim: Paired-end reads simulator
-
-------------------------------------------------------------------------
-r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bam_tview.c
+ A /trunk/samtools (from /branches/dev/samtools:62)
-Move definition of bam_nt16_nt4_table so we can build without curses.
+Create trunk copy
------------------------------------------------------------------------
r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
projects / samtools.git / blobdiff