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ChangeLog
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commit be310f37e58a59490e7ea5bc50040cd077267feb
Author: Jie Wu % Zhang <[email protected]>
Date: Fri Jul 5 15:22:28 2013 +0000
minor edits in README
commit fb13570d0d00e60bea86efe9741cb92c180a6c2e
Author: Jie Wu % Zhang <[email protected]>
Date: Fri Jul 5 15:20:12 2013 +0000
minor change in README
commit 7a8ea38091c727f32486d162bc987614b6c26688
Author: Jie Wu % Zhang <[email protected]>
Date: Fri Jul 5 15:15:03 2013 +0000
allow mismatch when the query seq is long in single anchor and micro exon search
readme
version number
commit ac68a89b2b13a267e2d78bd0f3e0aa018d264b82
Author: Jie Wu % Zhang <[email protected]>
Date: Mon Jul 1 12:17:20 2013 -0400
bug fixes (band_width >1)
commit 516652f8f1c58d73adb94c53c0b69aab055cf91c
Author: Jie Wu % Zhang <[email protected]>
Date: Wed Jun 26 23:40:51 2013 -0400
removed kent src, rewrote BefFile.cpp
commit bc65cea24701bd8e163cac9a9dc9c2c0ae897d9a
Author: Jie Wu % Zhang <[email protected]>
Date: Wed Jun 26 18:01:50 2013 -0400
implemented overlaping seeds
default -w 15 with --word-max-overlap 1
commit 387795e3ed152e1f9389081aceef4549de5f94f5
Author: Jie Wu % Zhang <[email protected]>
Date: Mon Jun 24 17:46:28 2013 -0400
renamed: models/hg18.cfg -> models/hg.cfg
renamed: models/mm9.cfg -> models/mm.cfg
commit 7f9327a2f53f0619b3d2ac50b2fe0d6b23c3f0e3
Merge: 36cf804 047cd4f
Author: Jie Wu % Zhang <[email protected]>
Date: Mon Apr 22 17:17:17 2013 -0400
Merge branch 'master' of ssh://git.code.sf.net/p/ngs-olego/code
commit 36cf804c39c0a055740d15a2f989715357bfc1c3
Author: Jie Wu % Zhang <[email protected]>
Date: Mon Apr 22 17:16:22 2013 -0400
improvments on anchor size for double anchor search
commit 047cd4f0628b1eaa67baa9d6c055e1cc000c2bd1
Author: Jie Wu % Zhang <[email protected]>
Date: Sun Apr 14 10:42:38 2013 -0400
Updated Readme
commit a29dd67f56b7b2d19c9f92b8d41fd0cc6b2efa6c
Author: Jie Wu % Zhang <[email protected]>
Date: Sun Apr 14 04:22:50 2013 +0000
change default of --max-multi and -M
version 1.1.1
commit 751b25ecdc1ed023c8e794440d9ca854ab6c6167
Author: Jie Wu % Zhang <[email protected]>
Date: Fri Apr 12 21:21:17 2013 +0000
Speed improvment by filtering out some highly repetitive anchors by default, new option added "allow-rep-anchor"
commit cbcb16c9d2a3128158c21a73c555a5589f70904f
Author: Jie Wu <[email protected]>
Date: Sun Mar 31 21:18:50 2013 -0500
VERSION 1.1.0, README updated
commit b2d07a1d7a06d1915e5639f89215632b459c2067
Author: Jie Wu % Zhang <[email protected]>
Date: Sun Mar 31 04:54:52 2013 +0000
further fix for duplicate entries occurred on exonbody reads
commit 7f6db82c29ea83eea4ede79e68436a47452a9cd6
Author: Jie Wu <[email protected]>
Date: Sat Mar 30 17:31:52 2013 -0500
minor fix on -W
commit 3f25f8cc6650d4e4246ec53b976f244236ba52ce
Author: Jie Wu <[email protected]>
Date: Fri Mar 29 17:40:39 2013 -0500
fixed bug about duplicate alignment entries
fix a bug in sam2bed.pl
commit 02edaef61a39f63379f461d496802abb777d72bf
Author: Jie Wu <[email protected]>
Date: Fri Mar 29 13:50:45 2013 -0500
opitmize option -W
commit f7985783c75c2830c6c48db0522e04b13e187c05
Author: Jie Wu % Zhang <[email protected]>
Date: Sun Mar 24 16:46:13 2013 +0000
record the command and program version in PG
fix the bug for -e option
commit 65bba660e6e2e6ad311a7fce1d84a0ebe150431c
Author: Jie Wu % Zhang <[email protected]>
Date: Tue Mar 5 15:00:29 2013 -0500
bug fixed for regression_model_gen, "chr"
commit e769cec864489ff4b5110e9560919a7739fb1fe2
Author: Chaolin Zhang %Zhang <[email protected]>
Date: Mon Jan 14 23:15:51 2013 -0500
minor bug fix on in sam2bed; does not affect results
commit 5265602b15fcf0ac25710b216d6b4c336da5bec5
Author: Chaolin Zhang %Zhang <[email protected]>
Date: Thu Jan 10 13:10:41 2013 -0500
Add support for gzip input file for sam2bed.pl
commit 8268ae4661db699887ace7a5eaa0eb6216785bff
Author: Chaolin Zhang %Zhang <[email protected]>
Date: Tue Jan 8 11:04:37 2013 -0500
reorganized codes in sam2bed.pl
commit 37482a66a2e4e5c2cf6f57f13bbf489f8650042e
Author: wuj <[email protected]>
Date: Thu Dec 13 18:39:15 2012 -0500
fixes
commit ac3b25ac2434e470ec5c2a1482cbf249ef3fcccf
Merge: 8b94500 6a2d2a4
Author: Chaolin Zhang %Zhang <[email protected]>
Date: Wed Dec 12 03:58:24 2012 +0000
Merge branch 'master' of ssh://[email protected]/p/ngs-olego/code
Conflicts:
bed2junc.pl
commit 8b945004bc621973bcdb74088c620acb4aa1c1fb
Author: Chaolin Zhang %Zhang <[email protected]>
Date: Wed Dec 12 03:51:20 2012 +0000
corrected the version number (1.0.8)
commit 6a2d2a4e64294f4c0a7f90b523cf0951f62552f9
Author: Jie Wu <[email protected]>
Date: Tue Nov 20 16:56:09 2012 -0600
final edits for v1.0.8
commit 9a547ccd8bf646450d809a1afe859b62844a9df2
Author: Jie Wu <[email protected]>
Date: Tue Nov 20 16:46:15 2012 -0600
improved the hit clustering step.
commit 224e722aa4e47e3baf3eee24279d31ef8ba50668
Author: wuj <[email protected]>
Date: Sun Oct 28 09:57:26 2012 -0400
some minor fixs, and added pipe support for mergePEsam.pl
commit d86754a7f7449891c065b1eecc5ee2b965f97988
Author: wuj <[email protected]>
Date: Fri Oct 26 15:26:51 2012 -0400
edits in readme
commit 63db9e493b0b5d5436013c548f4986cd5c39865e
Author: Jie Wu <[email protected]>
Date: Tue Oct 23 19:48:44 2012 -0500
fixed the overestimation problem in counting the mismatches when searching splice sites inside an "exon", the redundant counted diffs are now substracted from the total diff. However, there is still potential over counting at the end of the reads.
commit 757302a2d24f203684f3fcd6e7aee652dee3d04a
Author: Jie Wu <[email protected]>
Date: Fri Oct 12 15:48:12 2012 -0500
minor fix
commit 067acefe9ad0b48f8a647bc6a2e903709d826b9e
Author: Jie Wu <[email protected]>
Date: Fri Oct 12 12:44:26 2012 -0500
fixed a bug in merging, reverse & complimentary the seqs when the XA strand != the strand of the main entry
commit 58bdd1de3830f8586bc2eb14de4fa1122789609c
Author: Jie Wu <[email protected]>
Date: Thu Oct 11 12:35:36 2012 -0500
fixed a bug, XS tag not assigned for XA exon body reads
commit a3832a323b3d5526ec494944c899138e3f199f31
Merge: b84eb31 e5f8b83
Author: wuj <[email protected]>
Date: Tue Oct 9 19:47:07 2012 -0400
Merge commit 'e5f8b83'
commit e5f8b835476d58c12d79dee18c4a9715ef714084
Author: wuj <[email protected]>
Date: Tue Oct 9 19:42:59 2012 -0400
allow pipe for bed2junc.pl sam2bed.pl
commit b84eb317dd0a64179d3d19360ac28a379094f538
Merge: 0e278f0 b40ac5e
Author: Chaolin Zhang <[email protected]>
Date: Thu Sep 20 17:49:48 2012 -0400
Merge branch 'master' of ssh://git.code.sf.net/p/ngs-olego/code
commit 0e278f02e0e9716c01e57d287413e2e845a4b4c9
Author: Chaolin Zhang <[email protected]>
Date: Thu Sep 20 17:48:56 2012 -0400
minor fix in usage information of jigsawindex.c
commit b40ac5e903048e2b3f21859fe440a68cce57df3b
Author: wuj <[email protected]>
Date: Thu Aug 9 13:35:43 2012 -0400
1.0.6
Added option --max-multi (default:1000) to avoid huge data in a single line.
Added option --num-reads-batch.
Fixed a bug in the junction connecting step.
commit cc2b0213cea7d9251c8553c9be2bee4b2e0085bf
Author: wuj <[email protected]>
Date: Mon Jul 16 16:17:13 2012 -0400
version number change
commit f59a5c97d09e4538b22eca1e8d260f30752eddd9
Author: wuj <[email protected]>
Date: Mon Jul 16 15:59:04 2012 -0400
modified: ChangeLog
commit defd1572e058d65086fd544e5524a7edc1a55aad
Author: wuj <[email protected]>
Date: Mon Jul 16 15:54:08 2012 -0400
v1.0.5 (minor bug fixed)
commit 7590a6e4c0ee1c98a9ab26d4ce4cec1bafc61be5
Author: wuj <[email protected]>
Date: Sat Jun 16 00:04:08 2012 -0400
minor change
commit f9be7e4c77fb8208f74c58cf1ece212d94f88802
Author: wuj <[email protected]>
Date: Wed Jun 13 13:37:45 2012 -0400
changes in sam2bed to allow separate BED outputs for PE data
commit 0309e5b34d476ee93a7e6abf872a16f18ac1768a
Author: Chaolin Zhang <[email protected]>
Date: Tue Jun 12 16:35:46 2012 -0400
removed the -c option in olegoindex
commit 478722413655017574e5970b6f0f2d364e035774
Author: Chaolin Zhang <[email protected]>
Date: Tue Jun 12 09:19:22 2012 -0400
very minor change, aligned the usage information
commit f7d3d0b82100c29de3f0dfc4aa023250713f2496
Author: wuj <[email protected]>
Date: Mon Jun 11 22:42:26 2012 -0400
monor changes
commit 8f0bdcb00a0acda14f5e611368041f61aa455ff3
Author: wuj <[email protected]>
Date: Mon Jun 11 22:30:38 2012 -0400
v1.0.4, please see details in ChangeLog
commit 4448f51e9c6458da6b21c5b491eba3cc356820ec
Author: wuj <[email protected]>
Date: Sun Jun 10 14:50:51 2012 -0400
version 1.0.3
commit da0700bb4710da5f86855a92757bb6f41e58b31e
Author: wuj <[email protected]>
Date: Wed May 16 11:06:53 2012 -0400
new file: ChangeLog
modified: README
modified: jigsaw.cpp
commit 8ad7c0314f3eeeec2134a7278f44c862e289826b
Author: Chaolin Zhang <[email protected]>
Date: Tue May 15 21:46:57 2012 -0400
small fix in README
commit d1c178dadb0e71e364846247039418f65a2690ae
Author: Chaolin Zhang <[email protected]>
Date: Tue May 15 21:42:15 2012 -0400
removed some obsolete files
commit cafeaa4ec959816aefb314ecde64b453927fbdd4
Author: wuj <[email protected]>
Date: Tue May 15 16:20:35 2012 -0400
The v1.0.0 release
commit d94e44c3ed481090909604dd4e3f56cda4b46495
Author: wuj <[email protected]>
Date: Tue May 8 09:58:25 2012 -0400
modified: Makefile
modified: README
new file: bwa_files/ChangeLog
new file: bwa_files/NEWS
new file: bwa_files/bwa.1
new file: bwa_files/solid2fastq.pl
modified: common.mk
modified: cz/makefile
modified: jigsaw.cpp
modified: kent/makefile
deleted: ChangeLog
deleted: NEWS
deleted: bwa.1
deleted: solid2fastq.pl
commit be1b0cbfd27a32ff9f042fece58b3a1447ef36f3
Author: wuj <[email protected]>
Date: Thu May 3 17:02:14 2012 -0400
OLego files for public, version on 2012.05.03
commit 97f34f9c85308cd83754c5689b72196360ef9d61
Author: Chaolin Zhang <[email protected]>
Date: Mon Feb 27 23:05:50 2012 -0500
olego files for public