Non paired reads #31
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Non paired reads #31
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The assumption that the first value column on the `cov` object is a score column does not hold when running fragCounter with `paired=FALSE` - see the logic in `PrepareCov` where a different bamUtils function is used. The `count` column is set in that branch though and is the correct column to use here. Preserving the initial logic if `count` column does not exist though in case other usages depend on that behavior.
Passes `mc.cores` through to `PrepareCov` and then `bam.cov.gr` for potential speed-up. With default value of 1, `bam.cov.gr` was taking ~3 days for a 116x coverage single-end PacBio reads.
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Description:
Bug fix for single-end reads (paired=FALSE) & add mc.cores parameter.
Changes:
Commit 1:
Bug fix for running with paired=FALSE.
The assumption that the first value column on the
covobject is a score columndoes not hold when running fragCounter with
paired=FALSE- see the logic inPrepareCovwhere a different bamUtils function is used. The
countcolumn is set in that branchthough and is the correct column to use here.
Preserving the initial logic if
countcolumn does not exist though in case otherusages depend on that behavior.
Commit 2:
Add mc.cores argument to fragCounter.
Passes
mc.coresthrough toPrepareCovand thenbam.cov.grforpotential speed-up. With default value of 1,
bam.cov.grwas taking~3 days for a 116x coverage single-end PacBio reads.
Impact:
Allows fragCounter to be used with single-end reads and optionally run faster if using >1 cores.