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2018-12-19gridss: simplify preprocessing and rewrite using new pipe functionJustin Bedo
2018-12-18qsub: refactor overridingJustin Bedo
2018-12-12Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-12-12gridss: call identifyVariants through bionix treeJustin Bedo
2018-12-12Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-12-12gridss: refactor identify & annotate variantsJustin Bedo
2018-12-11Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-12-11samtools-sort: fix reversed link for identity sortJustin Bedo
2018-12-11gridss: fix softClipsToSplitReads after assemblyJustin Bedo
2018-12-10gridss: add java heapSize arguments.l-d-s
2018-12-10bowtie: initJustin Bedo
2018-12-10gridss: fix tmpdir bug.l-d-s
2018-12-06gridss: remove redundant collectGridssMetricsl-d-s
2018-11-29Correct argument for gridss option filel-d-s
2018-11-29gridss: fix for nix installations outside of /nixJustin Bedo
2018-11-26Also need config for 'assemble' step.l-d-s
2018-11-22Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-11-22gridss: restructure gridss pipelineJustin Bedo
2018-11-22samtools-sort: handle missing 'none' sorting caseJustin Bedo
2018-11-22gridss: fix configure file optional string errorJustin Bedo
2018-11-15Fix up gridss config file.l-d-s
2018-11-15gridss.softClipsToSplitReads: sort -> sortingl-d-s
2018-11-15Syntax.l-d-s
2018-11-15Need to test config != nulll-d-s
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
2018-11-12Function to great ini-style gridss config file.l-d-s
2018-11-07Fix to gridss.l-d-s
2018-11-07Add bwa to softClipsToSplitReadsl-d-s
2018-11-02Allow bwa-mem to take gzipped fastq inputsJustin Bedo
2018-11-02kallisto: initJustin Bedo
2018-11-01samtools-sort: don't sort if already sortedJustin Bedo
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.
2018-10-29bwa-mem: BWA output is query name sortedJustin Bedo
2018-10-29init: samtools-markdupJustin Bedo
2018-10-29init: samtools-fixmateJustin Bedo
2018-10-26init: mutectJustin Bedo
2018-10-26init: samtools-dictJustin Bedo
2018-10-25Improve type safety of samtools-mergeJustin Bedo
2018-10-25Simplify types for sortingJustin Bedo
2018-10-24Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-10-24Add merge to samtools.l-d-s
2018-10-24Fix platypus bugJustin Bedo
2018-10-23Allow building bwa-mem with one coreJustin Bedo
2018-10-23Simplify infercnv-appJustin Bedo
2018-10-23Wrap inferCNVJustin Bedo
Resolves #8
2018-10-08Add identity to compression functionsJustin Bedo
2018-10-08Fix type in samtools-viewJustin Bedo
2018-10-05implement typesJustin Bedo
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