cljam.io.sam.util.header — cljam 0.8.3

Utility functions for SAM header.

into-header clj

order-coordinate clj

order-queryname clj

order-unknown clj

order-unsorted clj

parse-header clj

(parse-header s)

Parse a header string, returning a map of the header.

parse-header-line clj

(parse-header-line line)

e.g. "@SQ SN:ref LN:45" => [:SQ {:SN "ref" :LN 45}]

sort-order clj

(sort-order header)

Returns sorting order of the sam as Keyword. Returning order is one of the following: :queryname, :coordinate, :unsorted, :unknown.

sorted-by clj

(sorted-by order header)

Replaces the sorting order field in SAM header.

sorted? clj

(sorted? header)

Returns true if the sam is sorted, false if not. It is detected by @HD SO:*** tag in the header.

stringify-header clj

(stringify-header hdr)

update-version clj

(update-version header)

Overwrites format version in SAM header.