Bug fixes and updates to be consistant with VarDictJava
Bug fixes and updates to be consistant with VarDictJava

A few chages:
1. The default filter -F is "0x504" instead of "0x500".  Now any
secondary alignment, PCR or optical duplicates, as well as unmapped
reads are filtered.
2. Complext variants extention $VEXT default to 2 instead of 3 to keep
within a codon length.  It can be changed by option "-X".
3. Phasing is now also extended to non-consecutive mismatches, allowing
$VEXT matches in between (lines 1777-1795
4. Fix the output column issue in paired analysis in lines 523-530, 557
and 561.
5. Fix CIGAR modification issue in line 1091.
6. Fix the indels at exon edge in RNA-seq due to alinger's error in
hisat2, which can produce negative coverages in some cases. They'll be
ignored.  (lines 1511-1514 and 1615-1618)
7. Prevent relignment to coop up soft-clip reads due to a couple of
rogue alignments due to sequencing error (added lines 4329 and 4345).

AstraZeneca-NGS/VarDict,AstraZeneca-NGS/VarDict,AstraZeneca-NGS/VarDict