Fixed a div/0 error that occured with a low-coverage sample.

DKFZ-ODCF / AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs

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Closed vinjana closed 5 years ago

vinjana commented 5 years ago

... in flags_isizes_PEaberrations.pl
Turned from <> idiom to eof()+getline() idiom for improved runtime-stability and error reporting.
Some code-layout fixes.
Use $ variables rather than old FH names and substituted context-dependent $_ variable occurrences by something more informative.
Some fixes in the bwaErrorCheck.sh script

Everything tested on one sample that failed due to lack of quality reads.