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Created with Raphaël 2.2.024Jun23221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159Code gussyingUpdated tagBam help so that it actually works...Added -f to tagBam.Pushed tagBam to GitHubAdded -counts option to coverageBed to only collect the count of overlaps (no pct., etc.)multiBamCov tweakAdded minQual (-q) and force proper pairs (-p) to multiBamCov.Added BamTools object cleanup to the Makefile.Clean Bamtools objectsTweaked Makefile and using GetNextAlignment() in multiBamCov.make Bamtools/lib on the flymake Bamtools/lib on the flyaded Bamtools/libaded Bamtools/libFirst cut at new multiBamCov tool. I like.Hooray, support for BamTools 1.0. Many good things to come.specifically request unpadded and 1-based ends from GetEndCoordinate()bamtools GetEndPosition() now defaults to unpadded, zero-basedSet BAM compression mode before openingremoved multiBamCov from main Makefileintersect, window, and gcB support for bamtools1.0coverageBed links with bamtools1.0bedToBam links with bamtools1.0preliminary support for bamtools1.0 for bamToBed.New BamTools 1.0 project structure and MakefileAdded BamTools-Ancillary filesChanged newline to tab in bamToBed for -tag -bed12.Further tweak to UCSC mysql help.Fixed multi-line UCSC mysql query in the help for multiple tool. Thanks to Brent Pedersen\!Patched Assaf Gordon's tweaks to gCB.Tweaked header in nucBedheader and custom pattern search for nucBed. Thanks to Can Alkan.Added output description to nucBed helpImprovements to closestBed. Thanks to suggestions by Brent Pedersen, Ryan Layer, Assaf Gordon, Dan Webster.mergeBed now _always_ reports in BED format (i.e., zero-based starts), regardless of input type.Added -5, -3, -trackline, -trackopts, and -dz options to genomeCoverageBed. Many thanks to Assaf Gordon.First cut at nucBed - profiles DNA sequences defined by BED intervals.Tweaked Makefile and added notboth option to pairToPair.fastaFromBed warns of exceeding length of chromosome and of zero length features.Updated version and RELEASE_HISTORY for 2.12.0