[Bioc-sig-seq] matchPDict, fixed=FALSE; "walk_tb_nonfixed_subject(): implement me"

[Ludo Pagie]

hi all,

I'm trying to match 80bp reads to a construct, a sequence of +/-
550bp. The construct contains a strecth of N's, representing a
stretch of 20 random nucleotides. 

I constructed a pdict from the reads, and a DNAString from the
construct. When I run matchPDict with fixed=TRUE, all goes fine
and I get 1.2M matches. 

> construct_mindex <- matchPDict(pdict, DNAString(construct), max.mismatch=3)
> sum(countIndex(construct_mindex))
[1] 1280283


With fixed=FALSE I get the following error:

> construct_mindex <- matchPDict(pdict, DNAString(construct), max.mismatch=3, fixed=FALSE)
Error in .match.PDict3Parts.XString(pdict at threeparts, subject, max.mismatch,  :
  walk_tb_nonfixed_subject(): implement me

Is there a way around this non-implemented function? Or any
chance it will be implemented soon? Or am I missing something.

If you need more background let me know.

Ludo

> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-06-17
r52313)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
[1] ShortRead_1.7.7      Rsamtools_1.1.7
lattice_0.18-8
[4] GenomicRanges_1.1.12 Biostrings_2.17.7    IRanges_1.7.7

loaded via a namespace (and not attached):
[1] Biobase_2.9.0 grid_2.12.0   hwriter_1.2   tools_2.12.0