[Bioc-sig-seq] trimLRPatters: inconstitency re max.[LR]mismatch

[Simon Anders]

Hi Patrick

I've just tried to trim adaptors of my Solexa reads and got a bit 
puzzled about trimLRPatterns's max.Rmismatch argument.

Let's say I have two sequences as follows:

 > library(ShortRead)
[...]
 > subject <- DNAString( "CGCCGGCCGAAATTTAA" )
 > pattern <- DNAString( "AAATTTAAATTTAAATTT" )

These have a clear overlapping alignment without mismatch:

    CGCCGGCCGAAATTTAA               <- subject
             AAATTTAAATTTAAATTT     <- (right) pattern

    CGCCGGCCG                       <- trimmed subject

So, I would expect trimLRpattern to trim it to the given "trimmed 
subject" sequence. However:

 > trimLRPatterns( subject=subject, Rpattern=pattern )
   17-letter "DNAString" instance
seq: CGCCGGCCGAAATTTAA

As you can see, the subject untrimmed.

If I now specify allow for 10% mismatch, trimming works:

 > trimLRPatterns( subject=subject, Rpattern=pattern, max.Rmismatch=.1 )
   9-letter "DNAString" instance
seq: CGCCGGCCG

Why do I need to allow for mismatches?


This here is even a bit stranger: COmpare the result of allowing for 
very small mismatches, say 10^-10, with exactly 0:

 > trimLRPatterns( subject=subject, Rpattern=pattern,
+    max.Rmismatch=1e-10 )
   9-letter "DNAString" instance
seq: CGCCGGCCG

 > trimLRPatterns( subject=subject, Rpattern=pattern,
+    max.Rmismatch=0 )
   17-letter "DNAString" instance
seq: CGCCGGCCGAAATTTAA

This is a bit dis-continuous, isn't it? ;-)


Cheers
   Simon

 > sessionInfo()
R version 2.11.0 Under development (unstable) (--)
x86_64-unknown-linux-gnu

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_1.5.15   lattice_0.17-26    BSgenome_1.15.4 
Biostrings_2.15.21
[5] IRanges_1.5.46

loaded via a namespace (and not attached):
[1] Biobase_2.7.2 grid_2.11.0   hwriter_1.1   tools_2.11.0


+---
| Dr. Simon Anders, Dipl.-Phys.
| European Molecular Biology Laboratory (EMBL), Heidelberg
| office phone +49-6221-387-8632
| preferred (permanent) e-mail: sanders at fs.tum.de