Structure Sam

A complete SAM data set that can be contained in a SAM file.
See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1.
The struct sam has a default constructor make-sam.
Accessor sam-header of type sam-header refers to the header.
Accessor sam-alignments of type list of sam-alignment refers to the read alignments.

Part of:

package elprep

Direct Method

get-output-functionsSets up the output thread, feeds the given header to the output data set, and returns four functi...
run-pipelineReads a SAM data set from input, applies filters to the header and the alignments,
and writes...
run-pipeline-in-situApplies filters destructively and returns the first argument.
This is like run-pipeline, exce...