Returns the base that was deleted at a position.
Returns the base that was deleted at a position.
Reference based position.
The base that was deleted at this position in the reference.
Returns the end position of the record described by this MD tag.
Returns the end position of the record described by this MD tag.
The reference based end position of this tag.
Given a read sequence, cigar, and a reference start position, returns the reference.
Given a read sequence, cigar, and a reference start position, returns the reference.
The base sequence of the read.
The cigar for the read.
The starting point of this read alignment vs. the reference.
A string corresponding to the reference overlapping this read.
Given a read, returns the reference.
Given a read, returns the reference.
A read for which one desires the reference sequence.
A string corresponding to the reference overlapping this read.
Returns whether this read has any mismatches against the reference.
Returns whether this read has any mismatches against the reference.
True if this read has mismatches. We do not return true if the read has no mismatches but has deletions.
Returns whether a base is a match against the reference.
Returns whether a base is a match against the reference.
Reference based position to check.
True if base matches reference. False means that the base may be either a mismatch or a deletion.
Returns the mismatched base at a position.
Returns the mismatched base at a position.
Reference based position.
The base at this position in the reference.
Returns the start position of the record described by this MD tag.
Returns the start position of the record described by this MD tag.
The reference based start position of this tag.
Converts an MdTag object to a properly formatted MD string.
Converts an MdTag object to a properly formatted MD string.
MD string corresponding to [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)
http://zenfractal.com/2013/06/19/playing-with-matches/