Dsl2/filter sv blacklist

[anoronh4]

Improvements to filtering:

• Added bed/bedpe files used by pcawg to filter results:
  • svBlacklistBed
  • svBlacklistBedpe
  • svBlacklistFoldbackBedpe
  • svBlacklistTEBedpe
• svBlacklist* files from above are sourced from pcawg_sv_merge data files. Their usage was modeled after the pcawg6_sv_merge_master.sh script from the same repo.
• parallelized iAnnotateSV, and defined resource configuration of .*AnnotateSVBedpe processes to improve runtime.
• Fixed header of bedpe, because svtools misreads certain lines with special characters, issue made here: bedpetovcf does not work with vcftobedpe output as input hall-lab/svtools#324
• The filtering scripts pair_to_pair_annot.py and pair_to_bed_annot.py converged into and were replaced by filter_regions_bedpe.py. The name change makes the intention of the script more obvious.
• added print statements and exception handling to python scripts to improve logging/debugging.

[gongyixiao]

Suggestion: You might want to put signatures on codes which written by you @anoronh4 . Up to you.

[gongyixiao]

Why am I seeing both filter_regions_bedpe.py and pair_to_pair_annot.py in the container folder together and they are not the same? And what was the file pair_to_bed_annot.py which is deleted here?

[anoronh4]

Why am I seeing both filter_regions_bedpe.py and pair_to_pair_annot.py in the container folder together and they are not the same? And what was the file pair_to_bed_annot.py which is deleted here?

pair_to_pair_annot.py and pair_to_bed_annot.py were supposed to have converged into and been replaced by filter_regions_bedpe.py. I forgot to remove pair_to_pair_annot.py. it's now removed and i changed the PR summary to better describe the changes.

Suggestion: You might want to put signatures on codes which written by you @anoronh4 . Up to you.

Will do!