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Created with Raphaël 2.2.024Oct2111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159chromsweep 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.Proper Gzip checkUpdated gzip detection. Weaker, but necessary for FIFO supportGzip detected by file extension. Weak, but only approach that works at this point.