1. 10 Mar, 2010 1 commit
  2. 04 Mar, 2010 1 commit
    • Aaron's avatar
      Version 2.5.4 (Mar-3-2010) · 6464b947
      Aaron authored
      	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!
      6464b947
  3. 19 Feb, 2010 2 commits
    • Aaron's avatar
      Fixed compilation warning in bamToBed.cpp · 6878bb24
      Aaron authored
      6878bb24
    • Aaron's avatar
      Version 2.5.3 (Feb-19-2010) · 19a7d197
      Aaron authored
      	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.
      19a7d197
  4. 12 Feb, 2010 1 commit
    • Aaron's avatar
      Fixed several bugs and improved BAM performance. · 2fe5a837
      Aaron authored
      	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.
      2fe5a837
  5. 06 Feb, 2010 1 commit
    • Aaron's avatar
      Changed "notboth" logic in pairToBed when inout is BAM. · 187c6749
      Aaron authored
      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.
      187c6749
  6. 03 Feb, 2010 1 commit
    • Aaron's avatar
      Version 2.5.2 (Feb-2-2010) · e5007f9c
      Aaron authored
      	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.
      e5007f9c
  7. 28 Jan, 2010 5 commits
  8. 23 Jan, 2010 3 commits
  9. 19 Jan, 2010 1 commit
  10. 11 Jan, 2010 7 commits
  11. 10 Jan, 2010 5 commits
  12. 08 Jan, 2010 4 commits
  13. 07 Jan, 2010 2 commits
  14. 06 Jan, 2010 1 commit
  15. 05 Jan, 2010 5 commits