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Unidirectional wgbs read reordering #43

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merged 7 commits into from
Feb 18, 2019

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vinjana
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@vinjana vinjana commented Feb 15, 2019

Analysis of undirectional WGBS data can improved by estimating the most likely orientation. To this aim the already existing WGBS_read_pair_reconstruction.py script was updated and integrated into the workflow

  • extensive refactoring including a solution for deconvoluting pipe-chains
  • import of code from the BamToFastqWorkflow (on the long run this library code should maybe go to another library or the DefaultPlugin -- but not now ... no time)

@vinjana vinjana requested a review from dankwart-de February 15, 2019 13:44
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@@ -178,6 +184,7 @@ waitForRegisteredPids_BashSucksVersion() {
jobs
declare -a realPids=$(listPids)
if [[ -v realPids && ${#realPids[@]} -gt 0 ]]; then
# TODO Make this a look and report the exact pid that failed (or the key, after switching from array to dictionary).
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Make this a look?

@vinjana vinjana merged commit fba38f0 into ReleaseBranch_1.2.73 Feb 18, 2019
@vinjana vinjana deleted the unidirectional-wgbs-read-reordering branch February 18, 2019 15:41
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