PAVFinder 0.4.2 (Oct 23, 2017)

Changes to improve robustness of tap.py

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Release Notes

State	Final release
License	BCCA (academic use)
Release Manager	Readman Chiu

This release includes a minor change in the part of the code that uses sub-sequence for filtering potential chimeras. It also includes minor changes that solidify tap.py for running the TAP(Targeted Assembly Pipeline).

Change log

1. chimera subseq checking improvements/fixes: determine subseq length from fasta file instead of cigar string in BAM file (hard-clip creates problem), multi-map checking requires mapping of entire sequence instead of just checking targets
2. requires samtools version >= 1.0 because samtools sort command changes
3. creates ruffus history file in output directory
4. explicity index fasta file after merging is done and before analysis scripts are run
5. determine num_proc parameter for running find_sv.py
6. changed name of one of duplicated format_read_pairs() functions
7. fixed bug if suppl_annot is not str