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Created with Raphaël 2.2.06Jan5427Dec26252417162Nov131Oct14Aug1311226Jul252429Jun2726258May16Mar1515Feb1413Jan121110529Nov21201918171615141031Oct30292827262524232220181711109876543130Sep28272620131289May26Apr25242115Mar310Feb83231Jan262529Dec2728Nov218Update R script output.Fix names in motif search and adding summits files.Add summits and remove extra names in files.Shorten and update file names.Shorten and update file names.Update cross correlation filenames to be shorter.Change sample names for convert reads.Update file names and output for filter reads.Fix merge of tests.verify that output directory doesn't exist.Fix test options and files that should be moved over.fix missing genome params and annotate peaks syntax.Update mapped reads with sample id.Add test for sample and experiment id conformance.Change fastq's to be new sample names as defined by the sample_id.Reslove merge conflicts.Merge branch '22_output_dir' into 'master'Update outdir default.Merge branch 'master' into '22_output_dir'Merge branch '25_pairedend_QC' into 'master'Remove test code.Change output of diffPeaks design file.Add option for outdir.Test for new unique experiment determination.Add in test to see if output exists.Change to int for fragment length.Change order of process. Made diffPeaks a when opperative.Change test lenght of output.Add in extension to other functions.Defaulted to zcat instead of unzip file.Fix paried-end quality output options.Fix paried-end quality output.remove annotate peak vennpie and update test.Fix memechip output directoires.Fix merge conflicts.Add test for motif search output.Check differential peaks.Remove testing design string.Fix tests so they run on single end and paired end.Fix motif search and limit number of peaks.