commit 9a547ccd8bf646450d809a1afe859b62844a9df2
Author: Jie Wu <wuj@cshl.edu>
Date:   Tue Nov 20 16:46:15 2012 -0600

    improved the hit clustering step.

commit 224e722aa4e47e3baf3eee24279d31ef8ba50668
Author: wuj <wuj@cshl.edu>
Date:   Sun Oct 28 09:57:26 2012 -0400

    some minor fixs, and added pipe support for mergePEsam.pl

commit d86754a7f7449891c065b1eecc5ee2b965f97988
Author: wuj <wuj@cshl.edu>
Date:   Fri Oct 26 15:26:51 2012 -0400

    edits in readme

commit 63db9e493b0b5d5436013c548f4986cd5c39865e
Author: Jie Wu <wuj@cshl.edu>
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 <wuj@cshl.edu>
Date:   Fri Oct 12 15:48:12 2012 -0500

    minor fix

commit 067acefe9ad0b48f8a647bc6a2e903709d826b9e
Author: Jie Wu <wuj@cshl.edu>
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 <wuj@cshl.edu>
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 <wuj@cshl.edu>
Date:   Tue Oct 9 19:47:07 2012 -0400

    Merge commit 'e5f8b83'

commit e5f8b835476d58c12d79dee18c4a9715ef714084
Author: wuj <wuj@cshl.edu>
Date:   Tue Oct 9 19:42:59 2012 -0400

    allow pipe for bed2junc.pl sam2bed.pl

commit b84eb317dd0a64179d3d19360ac28a379094f538
Merge: 0e278f0 b40ac5e
Author: Chaolin Zhang <zhangc@okito.rockefeller.edu>
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 <zhangc@okito.rockefeller.edu>
Date:   Thu Sep 20 17:48:56 2012 -0400

    minor fix in usage information of jigsawindex.c

commit b40ac5e903048e2b3f21859fe440a68cce57df3b
Author: wuj <wuj@cshl.edu>
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 <wuj@cshl.edu>
Date:   Mon Jul 16 16:17:13 2012 -0400

    version number change

commit f59a5c97d09e4538b22eca1e8d260f30752eddd9
Author: wuj <wuj@cshl.edu>
Date:   Mon Jul 16 15:59:04 2012 -0400

    	modified:   ChangeLog

commit defd1572e058d65086fd544e5524a7edc1a55aad
Author: wuj <wuj@cshl.edu>
Date:   Mon Jul 16 15:54:08 2012 -0400

    v1.0.5 (minor bug fixed)

commit 7590a6e4c0ee1c98a9ab26d4ce4cec1bafc61be5
Author: wuj <wuj@cshl.edu>
Date:   Sat Jun 16 00:04:08 2012 -0400

    minor change

commit f9be7e4c77fb8208f74c58cf1ece212d94f88802
Author: wuj <wuj@cshl.edu>
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 <zhangc@okito.rockefeller.edu>
Date:   Tue Jun 12 16:35:46 2012 -0400

    removed the -c option in olegoindex

commit 478722413655017574e5970b6f0f2d364e035774
Author: Chaolin Zhang <zhangc@okito.rockefeller.edu>
Date:   Tue Jun 12 09:19:22 2012 -0400

    very minor change, aligned the usage information

commit f7d3d0b82100c29de3f0dfc4aa023250713f2496
Author: wuj <wuj@cshl.edu>
Date:   Mon Jun 11 22:42:26 2012 -0400

    monor changes

commit 8f0bdcb00a0acda14f5e611368041f61aa455ff3
Author: wuj <wuj@cshl.edu>
Date:   Mon Jun 11 22:30:38 2012 -0400

    v1.0.4, please see details in ChangeLog

commit 4448f51e9c6458da6b21c5b491eba3cc356820ec
Author: wuj <wuj@cshl.edu>
Date:   Sun Jun 10 14:50:51 2012 -0400

    version 1.0.3

commit da0700bb4710da5f86855a92757bb6f41e58b31e
Author: wuj <wuj@cshl.edu>
Date:   Wed May 16 11:06:53 2012 -0400

    	new file:   ChangeLog
    	modified:   README
    	modified:   jigsaw.cpp

commit 8ad7c0314f3eeeec2134a7278f44c862e289826b
Author: Chaolin Zhang <czhang@rockefeller.edu>
Date:   Tue May 15 21:46:57 2012 -0400

    small fix in README

commit d1c178dadb0e71e364846247039418f65a2690ae
Author: Chaolin Zhang <czhang@rockefeller.edu>
Date:   Tue May 15 21:42:15 2012 -0400

    removed some obsolete files

commit cafeaa4ec959816aefb314ecde64b453927fbdd4
Author: wuj <wuj@cshl.edu>
Date:   Tue May 15 16:20:35 2012 -0400

    The v1.0.0 release

commit d94e44c3ed481090909604dd4e3f56cda4b46495
Author: wuj <wuj@cshl.edu>
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 <wuj@cshl.edu>
Date:   Thu May 3 17:02:14 2012 -0400

    OLego files for public, version on 2012.05.03

commit 97f34f9c85308cd83754c5689b72196360ef9d61
Author: Chaolin Zhang <zhangc@okito.rockefeller.edu>
Date:   Mon Feb 27 23:05:50 2012 -0500

    olego files for public
