A reply to a similar post also described removal of zero width reads;

"If you want to remove zero-width records before writing, then subset as

 xx[width(xx) != 0]"

So in your case something like;

nonZero     <- (width(trimmedCoords)!=0)
narrow(reads[nonZero], start=start(trimmedCoords)[nonZero],
end=end(trimmedCoords)[nonZero])

Marcus


On Sat, Mar 10, 2012 at 12:10 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 03/08/2012 04:40 PM, wang peter wrote:
>
>>        reads<- readFastq(fastqfile);
>>        seqs<- sread(reads);
>>        max.mismatchs<- mismatch_rate*1:nchar(**DNAString(PCR2rc))
>>        trimmedCoords<- trimLRPatterns(Rpattern = PCR2rc, subject = seqs,
>> max.Rmismatch= max.mismatchs, with.Rindels=T,ranges=T)
>>
>>  end(trimmedCoords)[1:20]
>>>
>>  [1] 22 18 20 33 14 22 22 20 22 22 22 15 20 37 19 13 20 22  0 34
>>
>>> start(trimmedCoords)[1:20]
>>>
>>  [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
>>
>> there is a "0" in the end of trimmedCoords so i cannot get the trimmed
>> sequences
>>
>
> The sequence has been trimmed entirely
>
> > as.character(Views(DNAString("**AA"), IRanges(1, 1)))
> [1] "A"
> > as.character(Views(DNAString("**AA"), IRanges(1, 0)))
> [1] ""
>
> Martin
>
>
>
>> trimmed3End<- narrow(reads, start=end(trimmedCoords), end=width(reads))
>>
>> R version 2.14.1 (2011-12-22)
>> Platform: x86_64-redhat-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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=C                 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_1.12.4    latticeExtra_0.6-19 RColorBrewer_1.0-5
>> [4] Rsamtools_1.6.3     lattice_0.20-0      Biostrings_2.22.0
>> [7] GenomicRanges_1.6.7 IRanges_1.12.6
>>
>> loaded via a namespace (and not attached):
>>  [1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0    grid_2.14.1
>>  [5] hwriter_1.3        RCurl_1.91-1       rtracklayer_1.14.4 tools_2.14.1
>>  [9] XML_3.9-4          zlibbioc_1.0.0
>>
>>
>
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