[BioC] report a problem (trimLRPatterns not symmetric?)

[Harris A. Jaffee]

The supposed counter-example (see below) suffers the same inherent  
defect as
in your last query: using 'with.*R*indels=T' with an 'Lpattern'.   
Fixing that
defect defeats the counter-example, unless I've missed something.

On Oct 11, 2011, at 11:55 AM, wang peter wrote:
> i found a wired problem, but i donot know if it is a bug
>
> triming from left is different from triming from right, please see  
> those
> coding
>
> such two sequence have distance of 3
> AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCA
> TCACATCACGATATCGTATGCCGTCTTCTGCTTG
>
>  AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
>
> subject<-
> DNAString 
> ("AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATA 
> TCGTATGCCGTCTTCTGCTTG")
> PCR2rc <-
> DNAString 
> ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG")
> trimLRPatterns(Rpattern = PCR2rc, subject = subject,
> max.Rmismatch=0.2,with.Rindels=T)
>  or trimLRPatterns(Rpattern = PCR2rc, subject = subject,
> max.Rmismatch=3,with.Rindels=T)
>   25-letter "DNAString" instance
> seq: AAAAAAAAAAAAAAACGACACAAGC
>
> such two sequence are symitric of those above
>
>  GATCGGAAGAGCACACGTCTGAACTCCA
> TCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC
> AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
>
> subject<-
> DNAString 
> ("GATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAA 
> AAAAAAAAACGACACAAGCCC")
> PCR2rc <-
> DNAString 
> ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG")
> trimLRPatterns(Lpattern = PCR2rc, subject = subject,
> max.Lmismatch=0.2,with.Rindels=T)
>
>  88-letter "DNAString" instance
> seq:
> ATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAA 
> AAAAAACGACACAAGCCC

But,

 > trimLRPatterns(Lpattern = PCR2rc, subject = subject,  
max.Lmismatch=0.2, with.Lindels=T)
   25-letter "DNAString" instance
seq: AAAAAAAAAAAAACGACACAAGCCC

>
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