- consolidateCigar
Need a well-formed, consolidated Cigar string so that the left aligning code
works properly. For exa
- calcAlignmentByteArrayOffset
- countBasesAtPileupPosition
Get the counts of bases at a genome location for a pileup
- createReadAlignedToRef
Aligns reads the haplotype, and then projects this alignment of read -> hap onto
the reference via t
- leftAlignIndel
Takes the alignment of the read sequence readSeq to the reference sequence
refSeq starting at 0-bas
- addCigarElements
Helper function for trimCigar that adds cigar elements (of total length X) of
elt.op to dest for X b
- applyCigarToCigar
Generate a new Cigar that maps the operations of the first cigar through those
in a second For examp
- calcFirstBaseMatchingReferenceInCigar
Get the offset (base 0) of the first reference aligned base in Cigar that occurs
after readStartByBa
- calcNumHighQualitySoftClips
Calculate the number of bases that are soft clipped in read with quality score
greater than threshol
- cigarHasZeroSizeElement
Does one of the elements in cigar have a 0 length?
- getBasesCoveringRefInterval
Get the byte[] from bases that cover the reference interval refStart -> refEnd
given the alignment o
- getNumAlignedBasesCountingSoftClips
Get the number of bases aligned to the genome, including soft clips If read is
not mapped (i.e., doe