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Handle case where read lengths are longer than fragment size 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4852 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-12-16 02:19:55 +00:00
parent a5e1854b3a
commit b1f0df0047
1 changed files with 4 additions and 1 deletions
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5
R/phasing/RBP_theoretical.R
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@ -69,8 +69,11 @@ pPairedEndReadsOfSpecificFragmentCanCoverHetPairAtDistance <- function(L, F, k)
stop("Cannot have fragments of size < 1")
}
# if F < L, then set the effective read length to be F:
L = pmin(L, F)
i = F - 2 * L
#print(paste("pPairedEndReadsOfSpecificFragmentCanCoverHetPairAtDistance(L= ", L, ", F= (", paste(F, collapse=", "), "), k= (", paste(k, collapse=", "), ")), i= (", paste(i, collapse=", "), ")", sep=""))
#print(paste("pPairedEndReadsOfSpecificFragmentCanCoverHetPairAtDistance(L= (", paste(L, collapse=", "), "), F= (", paste(F, collapse=", "), "), k= (", paste(k, collapse=", "), ")), i= (", paste(i, collapse=", "), ")", sep=""))
# If i < 0, then ASSUMING that overlapping region is identical, we can "pretend" to have 2 reads of length L and L+i, with no insert between them.
# Otherwise, leave i alone and L1 = L2 = L: