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Created with Raphaël 2.2.025Oct242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159Oops. Extra ;Fix typo in closestBed: -S for opposite strands, not -sAdded a signed distance option (-D) to closestBedchromsweep now obeys -s and -Schromsweep no longer overloads results p_q on chrom change.Tweaked Makefile for proper zlib inclusiongetBamBlocks no longer splits on D CIGAR ops when not wanted.Merge pull request #8 from daler/masterwindowBed -sm -> -SmMinor updates.Version 2.12.3fixed -bed in intersectBed with gzipped -b. Thanks to @daler.-bed now behaves when using bam input in intersectBed.Release 2.13.2Improved detection of faulty GFF features.Fixed mouse.mm9.genome. Thanks to Charles Plessy.Fixed major bug in intersectBed -split. Thanks to Sol Katzman.removed unused attributes in chromsweepReworked the nullBed logic.clean up chromsweep interfaceMoved nullBed reset to GetNextBedUpdated READMEUpdated READMEUpdated READMEUpdated READMEAdded newline before version.h EOFAdded new -sorted option to intersectBed. No memory and filthy fast.Gussy.chromsweep is a proper tool. Now to make it an iterable class.chromsweep is now a python-style generator. Big smile\!chromsweep demogcB no longer requires a genome file for BAM. New chromsweep tool.Changed error message when BAM is not qeury sorted in pairToBedAdded Seek and Rewind (destroy?) to BedFile.Added -scores option to tagBamFixed pairToPair's -type notBoth modeVersion 2.13.1: Added -s, -S, and -names to tagBam.Added -s, -S, and -names to tagBam.Avoid deleting bedStream iff stdinReasoning for GZIP detection change.