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Unidirectional wgbs read reordering #43
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vinjana
merged 7 commits into
ReleaseBranch_1.2.73
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unidirectional-wgbs-read-reordering
Feb 18, 2019
Merged
Unidirectional wgbs read reordering #43
vinjana
merged 7 commits into
ReleaseBranch_1.2.73
from
unidirectional-wgbs-read-reordering
Feb 18, 2019
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Origin: https://github.com/cimbusch/TWGBS, Commit: 4c196bad4bb44dc56166ede85d6e1d74de3eaf92
…inished unit tests.
…s (including backports from 1.3.0/develop).
vinjana
commented
Feb 15, 2019
resources/analysisTools/bisulfiteWorkflow/bwaMemSortSlimWithReadConversionForBisulfiteData.sh
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dankwart-de
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Feb 15, 2019
resources/analysisTools/bisulfiteWorkflow/WGBS_read_pair_reconstruction.py
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resources/analysisTools/bisulfiteWorkflow/bwaMemSortSlimWithReadConversionForBisulfiteData.sh
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…tions after review.
…rror robustness and handling.
dankwart-de
approved these changes
Feb 18, 2019
resources/analysisTools/bisulfiteWorkflow/bwaMemSortSlimWithReadConversionForBisulfiteData.sh
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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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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