cljam.io.sam.util.flag — cljam 0.8.3

Utility functions for SAM flags.

both-unmapped? clj

(both-unmapped? f)

Tests if both the segment and its mate segment are unmapped.

decode clj

(decode f)

Returns a set of keywords for a given flag integer.

encode clj

(encode flag-set)

Returns a flag integer encoding set of keywords.

encoded clj macro

(encoded flag-set-literal)

Macro to provide an encoded flag with set of keywords.

flag-keywords clj

flags clj

multiple? clj

(multiple? f)

Tests if the template has multiple segments.

primary? clj

(primary? f)

Returns true when an alignment with given flag is a primary line.

properly-aligned? clj

(properly-aligned? f)

Tests if the paired-end segments are properly aligned.

r1? clj

(r1? f)

Tests if the segment is the first in the template.

r1r2 clj

(r1r2 f)

Returns 0 for single-end, 1 for R1 and 2 for R2.

r2? clj

(r2? f)

Tests if the segment is the last in the template.

reversed? clj

(reversed? f)

Tests if the segment is reversed.

secondary? clj

(secondary? f)

Tests if the alignment is secondary.

unmapped? clj

(unmapped? f)

Tests if the segment is unmapped.