[FIX] Yara: post-align reads with an affine scoring scheme
[FIX] Yara: double cigar length estimate
[FIX] Yara: swapped contig and read in call to globalAlignment()
[INTERNAL] Yara: renamed getValue() as getMember() to avoid const ref problems
[FIX] Yara: clip semi-global alignments
[API] Gaps: added countLeading/TrailingGaps() and clipSemiGlobal()
[FIX] Yara: shrink matches after semi-global alignment
[FIX] Yara: revert doubling of cigar length estimate
[CLI] Yara: added option --rabema to output a SAM/BAM file containing rabema-compliant alignments/intervals
[TEST] Yara: updated test file
Merge pull request #498 from esiragusa/fix/yara/indels

Yara: improved alignment of indels