Are you working on this now Martin? I have started to implement
parsing of BAM files but right now my working is stalling a bit due to
some other commitments, like finishing my thesis.
Kasper
On Jul 24, 2009, at 19:09 , Martin Morgan wrote:
"Hattem, Gaye" <[email protected]> writes:
Does the readAligned function in ShortRead currently support the SAM
format? The vignette mentions that Short Read has been extended to
include several formats and lists the SAM format but I don't see
this option documented anywhere.
Hi Gaye --
SAM is not yet supported, but will be in the next release (my
preference is for the binary variant, BAM). MAQ and Bowtie-style input
is available.
Martin
Gaye Hattem
Stowers Institute for Medical Research
glh at stowers dot org
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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