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coverage: 67.531% (-0.4%) from 67.957%
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remove broken symlinks in runs; call CheckIlluminaDirectory (#640)

* remove broken symlinks in runs; call CheckIlluminaDirectory

HiSeq4000 and HiSeq X runs write out a single “s.locs” file to
Data/Intensities, rather than per-tile cluster location files within
Data/Intensities/L*/*.locs. Related to this, CheckIlluminaDirectory
with LINK_LOCS=‘true’ creates symlinks from where per-tile location
files would be to the absolute path of the s.locs file. This can cause
problems when moving a run to a new system, since the absolute paths
will be incorrect. This addition checks to see if s.locs is present. If
so, broken symlinks within the Data/Intensitites/L* are removed, and
LINK_LOCS is specified for the CheckIlluminaDirectory call that now
happens before demultiplexing. This call ensures the run looks correct,
and in the case of HiSeq4000/HiSeqX runs, also creates symlinks for
per-tile location files using absolute paths on the current system.
This is all something of a workaround for Broad-derived
HiSeq4000/HiSeqX runs, which are delivered with brittle absolute
symlinks. With this addition, runs from Broad walkup or elsewhere are
more cloud-compatible. In connection with this, a PR has been opened in
the Picard repository to request that LINK_LOCS can create relative
symlinks rather than absolute:
https://github.com/broadinstitute/picard/issues/877

* remove_broken_symlinks -> find_broken_symlinks, with logging changes

remove_broken_symlinks has been renamed to find_broken_symlinks since
it now returns a list of broken links rather than removing them
directly. The function in util.file is now silent, and logging is
performed where the function is called in illumina.py.

* pass link_locs as python bool

5183 of 7675 relevant lines covered (67.53%)

0.68 hits per line

Source Files on job 3878.1