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Commits on Apr 12, 2010
Commits on Mar 29, 2010
Commits on Mar 24, 2010
  1. Final changes for 2.6.0

    committed Mar 24, 2010
Commits on Mar 23, 2010
Commits on Mar 22, 2010
Commits on Mar 19, 2010
Commits on Mar 18, 2010
  1. Initial support for BED12 output in bamToBed.

    	1. Can parse CIGAR string.
    	2. Output looks roughly correct.  Need to continue testing.
    committed Mar 18, 2010
  2. Added new program: overlap

    committed Mar 18, 2010
  3. Now tracking bin/ and src/

    committed Mar 18, 2010
Commits on Mar 17, 2010
  1. Improvements to coverageBed

    	1. Added the -hist option (credit to Jose Bras).
    	2. Substantially improved the speed by using a depth iterator instead of copying the depth map for each feature in B when computing coverage.
    committed Mar 17, 2010
Commits on Mar 15, 2010
  1. Update to fastaFromBed and intersectBed.

    	1. Added the -wo option to intersectBed.
    	2. Added the -s option to fastaFromBed.
    committed Mar 15, 2010
Commits on Mar 12, 2010
  1. Fixed yet another bug in the -nms option in mergeBed.

    	Now using a map to track the unique names of the features in a merged block.
    	The consequence is that names will not be reported in the order they were added.
    committed Mar 12, 2010
Commits on Mar 10, 2010
Commits on Mar 4, 2010
  1. Version 2.5.4 (Mar-3-2010)

    	Fixed an insidious bug that caused malformed BAM output from intersectBed and pairToBed.  The previous BAM files worked fine with samtools as BAM input, but when piped in as SAM, there was an extra tab that thwarted conversion from SAM back to BAM.  Many thanks to Ivan Gregoretti for reporting this bug.  I had never used the BAM output in this way and thus never caught the bug!
    committed Mar 4, 2010
Commits on Feb 19, 2010
  1. Version 2.5.3 (Feb-19-2010)

    	1. Fixed bug to "re-allow" track and "browser" lines.
    	2. Fixed bug in reporting BEDPE overlaps.
    	3. Fixed bug when using type "notboth" with BAM files in pairToBed.
    	4. When comparing BAM files to BED/GFF annotations with intersectBed or pairToBed, the __aligned__ sequence is used, rather than the __original__ sequence.
    	5. Greatly increased the speed of pairToBed when using BAM alignments.
    	6. Fixed a bug in bamToBed when reporting edit distance from certain aligners.
    committed Feb 19, 2010
Commits on Feb 12, 2010
  1. Fixed several bugs and improved BAM performance.

    	1. Fixed bug to "re-allow" track and "browser" lines.
    	2. Fixed bug in reporting BEDPE overlaps.
    	3. Fixed bug when using type "notboth" with BAM files in pairToBed.
    	4. When comparing BAM files to BED/GFF annotations with intersectBed or pairToBed, the __aligned__ sequence is used, rather than the __original__ sequence.
    committed Feb 12, 2010
Commits on Feb 6, 2010
  1. Changed "notboth" logic in pairToBed when inout is BAM.

    Changed "notboth" logic in pairToBed when inout is BAM.
    Changed "notboth" logic in pairToBed when inout is BAM.
    Changed "notboth" logic in pairToBed when inout is BAM.
    Changed "notboth" logic in pairToBed when inout is BAM.
    Changed "notboth" logic in pairToBed when inout is BAM.
    Changed "notboth" logic in pairToBed when inout is BAM.
    Changed "notboth" logic in pairToBed when inout is BAM.
    committed Feb 6, 2010
Commits on Feb 3, 2010
  1. Version 2.5.2 (Feb-2-2010)

    	1. The start and end coordinates for BED and BEDPE entries created by bamToBed are now based on the __aligned__ sequence, rather than the original sequence.  It's obvious, but I missed it originally...sorry.
    	2. Fixed a bug in bamToBed that caused a crash when created BED / BEDPE from "spliced" BAM alignments.
    	3. Added an error message to mergeBed preventing one from using "-n" and "-nms" together.
    	4. Fixed a bug in pairToBed that caused neither -type "notispan" nor "notospan" to behave as described.
    committed Feb 3, 2010
Commits on Jan 28, 2010
  1. Fixed line parsing bug.

    	1. atoi fails in parseLine when start = 0.  Changed to strtol.
    	2. modified parseBedLine and parseGffLine to do better sanity checking.
    committed Jan 28, 2010
  2. Version 2.5.0

    committed Jan 28, 2010
  3. Fixed bug in pairToBed and removed tr1 include.

    	1. pairToBed had a bug in the way it parsed -a
    	2. extraneous tr1/unordered_map include in bedfile.h causes compile issues on some machines.
    committed Jan 28, 2010