3,045
edits
Changes
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* Update dedup, recab, qplot, & verifyBamID steps to be specified via configuration
* Update dedup, recab, qplot, & verifyBamID steps to be specified via configuration
** Easier to insert steps between/before/after these
** Easier to insert steps between/before/after these
** Use PER_MERGE_STEPS to disable any of these steps (see gotcloudDefaults.conf for its default setting)
*** RUN_QPLOT and RUN_VERIFY_BAM_ID are only used for validating executable/reference existence and will be deprecated completely soon
* Fixed bug where the merge failed if there was only 1 fastq pair
* Fixed bug where the merge failed if there was only 1 fastq pair
* Improve informational messages
* Improve informational messages
* Update to always require REF
* Update to always require REF
** this fixes bug that ''ldrefine'' was not checking REF or adding the optional prefix to it.
** this fixes bug that ''ldrefine'' was not checking REF or adding the optional prefix to it.
* SVM - fib bug on qual check in run_libsvm.pl
* SVM - fix bug on qual check in run_libsvm.pl
* Update defaults for filtering
* Update defaults for filtering
* Fixed bug in libVcf/VcfFile that had FamID instead of FatID
* Fixed bug in libVcf/VcfFile that had FamID instead of FatID
