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2018-12-11Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-12-11gridss: fix softClipsToSplitReads after assemblyJustin Bedo
2018-12-10gridss: add java heapSize arguments.l-d-s
2018-11-29Correct argument for gridss option filel-d-s
2018-11-22gridss: restructure gridss pipelineJustin Bedo
2018-11-22gridss: fix configure file optional string errorJustin Bedo
2018-11-15gridss.softClipsToSplitReads: sort ordering is not preservedJustin Bedo
NB: this breaks gridss.preprocessBam
2018-11-13Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-11-12Attempt to integrate config file into GRIDSS stagel-d-s
2018-11-07Add bwa to softClipsToSplitReadsl-d-s
2018-10-29Split gridss into constituentsJustin Bedo
Wrap each individual command for GRIDSS so that bionix executed the pipeline rather than GRIDSS. This patch introduces a "call" function that executed the whole pipeline in bionix on an arbitrary BAM file. Resolves #10.
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