Opened 8 months ago

Closed 8 months ago

#962 closed request (fixed)

Aligner::Cigar(string) constructor

Reported by: Peter Owned by: Jari Häkkinen
Priority: major Milestone: yat 0.19
Component: utility Version: trunk
Keywords: Cc:

Description

A constructor that can parse the output created by the ostream operator.

Change History (2)

comment:1 Changed 8 months ago by Peter

Milestone: yat 0.x+yat 0.19

comment:2 Changed 8 months ago by Peter

Resolution: fixed
Status: newclosed

In 4003:

Add a constructor Aligner::Cigar(string) (closes #962)

Add a function cigar_table, which is a wrapper around bam_cigar_table
from htslib, translating operation characters in a CIGAR such as 'M'
or 'I' into the value as they are stored in a Cigar object (or a bam
entry). Function, bam_cigar_table, not available in older versions of
htslib or when building --without-htslib, so implement our own version
and decide at configure time whether using homebrew or call htslib.

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