From a44dcfeb0588ab88a6aba77e3f561682a42c1d21 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 12 Jun 2009 14:33:42 +0000 Subject: [PATCH] update ChangeLog --- ChangeLog | 253 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 253 insertions(+) diff --git a/ChangeLog b/ChangeLog index fe2a947..6d10fed 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,256 @@ +------------------------------------------------------------------------ +r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines +Changed paths: + M /trunk/samtools/AUTHORS + M /trunk/samtools/Makefile + M /trunk/samtools/misc/Makefile + +fixed minor things in Makefile + +------------------------------------------------------------------------ +r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines +Changed paths: + M /trunk/samtools/bamtk.c + + * samtools-0.1.4-5 (r3310 + * no change to samtools itself. Version number is increased to reflect the + changes in the Makefile building system. + +------------------------------------------------------------------------ +r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines +Changed paths: + M /trunk/samtools/AUTHORS + D /trunk/samtools/README + +update information... + +------------------------------------------------------------------------ +r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/misc/novo2sam.pl + + * updated novoalign converter by Colin Hercus et al. + * this version works with indels + +------------------------------------------------------------------------ +r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/INSTALL + M /trunk/samtools/Makefile + M /trunk/samtools/misc/Makefile + M /trunk/samtools/zlib/Makefile + + * update Makefile + * update INSTALL instruction + +------------------------------------------------------------------------ +r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines +Changed paths: + A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325) + D /trunk/samtools/Makefile.am + D /trunk/samtools/Makefile.generic + D /trunk/samtools/Makefile.lite + D /trunk/samtools/autogen.sh + D /trunk/samtools/cleanup.sh + D /trunk/samtools/configure.ac + A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305) + D /trunk/samtools/misc/Makefile.am + D /trunk/samtools/misc/Makefile.generic + M /trunk/samtools/razf.c + A /trunk/samtools/zlib + A /trunk/samtools/zlib/Makefile + A /trunk/samtools/zlib/adler32.c + A /trunk/samtools/zlib/compress.c + A /trunk/samtools/zlib/crc32.c + A /trunk/samtools/zlib/crc32.h + A /trunk/samtools/zlib/deflate.c + A /trunk/samtools/zlib/deflate.h + A /trunk/samtools/zlib/gzio.c + A /trunk/samtools/zlib/infback.c + A /trunk/samtools/zlib/inffast.c + A /trunk/samtools/zlib/inffast.h + A /trunk/samtools/zlib/inffixed.h + A /trunk/samtools/zlib/inflate.c + A /trunk/samtools/zlib/inflate.h + A /trunk/samtools/zlib/inftrees.c + A /trunk/samtools/zlib/inftrees.h + A /trunk/samtools/zlib/trees.c + A /trunk/samtools/zlib/trees.h + A /trunk/samtools/zlib/uncompr.c + A /trunk/samtools/zlib/zconf.h + A /trunk/samtools/zlib/zlib.h + A /trunk/samtools/zlib/zutil.c + A /trunk/samtools/zlib/zutil.h + D /trunk/samtools/zutil.h + + * added zlib-1.2.3 as razip requires that + * prepare to changed back to the Makefile building system + * unfinished! (will be soon) + +------------------------------------------------------------------------ +r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + +Unfinished + +------------------------------------------------------------------------ +r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/bam_maqcns.c + M /trunk/samtools/bamtk.c + + * samtools-0.1.4-4 (r325) + * further avoid wrong consensus calls in repetitive regions. + +------------------------------------------------------------------------ +r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines +Changed paths: + M /trunk/samtools/bam_maqcns.c + M /trunk/samtools/bam_plcmd.c + M /trunk/samtools/bamtk.c + M /trunk/samtools/sam.c + M /trunk/samtools/sam.h + + * samtools-0.1.4-3 (r324) + * make maqcns generate the correct call in repetitive regions. + * allow filtering on mapQ at the pileup command line + +------------------------------------------------------------------------ +r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * samtools.pl-0.3.2 (r322) + * indels and SNPs use different mapping quality threshold + +------------------------------------------------------------------------ +r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines +Changed paths: + M /trunk/samtools/misc/export2sam.pl + +fixed a typo + +------------------------------------------------------------------------ +r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + +just typo. no real change + +------------------------------------------------------------------------ +r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + +a little bit code cleanup + +------------------------------------------------------------------------ +r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * samtools.pl-0.3.1 + * change default parameters + * optionally print filtered variants + +------------------------------------------------------------------------ +r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * samtools.pl-0.3.0 + * combine snpFilter and indelFilter + +------------------------------------------------------------------------ +r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * samtools.pl-0.2.3 + * change a default parameter + +------------------------------------------------------------------------ +r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 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/bamtk.c + M /trunk/samtools/sam.c + + * samtools-0.1.4-2 (r316) + * pileup: cap mapping quality at 60 (by default) + * pileup: always calculate RMS mapq + * pileup: allow to output variant sites only + +------------------------------------------------------------------------ +r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * samtools.pl-0.2.2 + * added pileup2fq + +------------------------------------------------------------------------ +r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * in snpFilter, suppress non-SNP sites + +------------------------------------------------------------------------ +r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * samtools.pl-0.2.1 + * fixed a typo + +------------------------------------------------------------------------ +r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines +Changed paths: + M /trunk/samtools/misc/samtools.pl + + * samtools.pl-0.2.0 + * snpFilter + +------------------------------------------------------------------------ +r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines +Changed paths: + M /trunk/samtools/bgzf.c + + * minor changes to bgzf: return NULL if fd == -1 + * suggested by {kdj,jm18}@sanger.ac.uk + +------------------------------------------------------------------------ +r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines +Changed paths: + A /trunk/samtools/misc/interpolate_sam.pl + +Script for paired-end pileup, contributed by Stephen Montgomery. + +------------------------------------------------------------------------ +r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines +Changed paths: + M /trunk/samtools/bamtk.c + M /trunk/samtools/sam.c + + * samtools-0.1.4-1 (r304) + * fixed a minor bug in printing headers + +------------------------------------------------------------------------ +r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines +Changed paths: + M /trunk/samtools/ChangeLog + M /trunk/samtools/NEWS + M /trunk/samtools/bam_plcmd.c + M /trunk/samtools/bamtk.c + M /trunk/samtools/misc/maq2sam.c + M /trunk/samtools/samtools.1 + +Release samtools-0.1.4 + ------------------------------------------------------------------------ r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines Changed paths: -- 2.39.2