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Created with Raphaël 2.2.016Dec8732128Nov2624232019181716151210543130Oct292292Merge branch 'master' into 'master'mastermasterEnhance the genetrack, cwpair2 and repmatch_gff3 tools to include theMerge branch 'master' into 'master'Update the bam_to_scidx .shed.yml file in preparation for release toMerge branch 'master' into 'master'Add a feature for hiding / displaying advanced options for theMerge branch 'master' into 'master'Changes to tool interfaces based on first review by the Pugh/MahonyMerge branch 'master' into 'master'Restrict output plot format to PDF for repmatch_gff3 tool.Make genetrack require Anaconda 2.3.0 instead of Numpy 1.9. Thid doesMerge branch 'master' into 'master'Eliminate the ability to sort by chromosome in the Cwpair2 tool since itAdd the bam_to_scidx tool.Merge branch 'master' into 'master'Restrict Cwpair2 plot output format to pdf only and correct the testRename the SsccIdx datatype to be ScIdx.Merge branch 'master' into 'master'Add .shed.yml file sin preparation for submitting to open source.Merge branch 'master' into 'master'Next round of fixes for all 3 tools. Genetrack must use optparse ratherMerge branch 'master' into 'master'Cleanup for the repmatch_gff3 tool.Add the production-ready version of the repmatch_gff3 tool. This toolLimit the functional test datasets for the cwpair2 tool to much smallerProduction-ready version of the cwpair2 tool along with test data for 2Removed GFF input support and worked on correcting the input files.Merge branch 'master' into 'master'Push changes to cwpair2 and repmatch_gff3 so Geoffrey can proceed withRemoved args parameter in genetrack.util.Merge branch 'master' into 'master'More finishing touches on the genetrack tool.Updated CWPair2 XML input parameters (WIP) and CWPAIR2_util.Removed large repmatch filesInitial cwpair2 files addedMerge branch 'master' into 'master'Enhancements to the genetrack tool to produce an output collection andMerge branch 'master' into 'master'Added smaller input and output test datasets for cwpair2 tool.Merge branch 'master' into 'master'