Opened 6 years ago

Closed 6 years ago

#859 closed request (fixed)

wrapper class around faidx_t

Reported by: Peter Owned by: Peter
Priority: major Milestone: yat 0.14
Component: omic Version:
Keywords: Cc:

Description

faidx_t is a struct in htslib (and libbam)

Create wrapper class or possibly two. One for the fasta index and one for holding the sequence.

Change History (2)

comment:1 Changed 6 years ago by Peter

Status: newassigned

comment:2 Changed 6 years ago by Peter

Resolution: fixed
Status: assignedclosed

(In [3475]) closes #859

New class handling Fasta files that have an index file (see samtools faidx). Allow easy random access to the Fasta file.

A new functor that calculates the genomic complement of a char, e.g. A -> T. A function using this functor on a range as well as combined with reverse to create reverse complement which is more common.

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