Just applied it to devel.

Thanks,
Michael

On Thu, Aug 30, 2012 at 5:17 PM, Ryan C. Thompson <rct@thompsonclan.org>wrote:

> So anyway, now that we've figured out the problem of sending the patch,
> can we discuss the merits of the patch itself? Currently I have to apply
> this patch to every update of rtracklayer in order to make it read GFF
> files generated by Cufflinks. I've been happily using rtracklayer with this
> patch applied for months.
>
>
>
> On 08/27/2012 10:24 AM, Ryan C. Thompson wrote:
>
>> Ok, I put the patch in a Github gist, since the list seems to not like
>> patch as an attachment:
>>
>> https://gist.github.com/**3490557 <https://gist.github.com/3490557>
>>
>> On 08/27/2012 09:32 AM, Ryan C. Thompson wrote:
>>
>>> It looks like the attachment was scrubbed from my initial message. Here
>>> is another attempt to send it.
>>>
>>> On Mon 27 Aug 2012 08:50:03 AM PDT, Ryan C. Thompson wrote:
>>>
>>>> Hi all,
>>>>
>>>> I recently found that rtracklayer's GFF3 file read was unable to read
>>>> GFF3 files produced by Cufflinks. I tracked the problem down to the
>>>> occurrence of equals signs in tag values. For example, the following
>>>> line was problematic:
>>>>
>>>> C123300344      Cufflinks       transcript      1       132 . -
>>>> .
>>>> ID=TCONS_00000337;geneID=XLOC_**000337;oId=ENSMMUP00000032229;**
>>>> nearest_ref=**ENSMMUP00000032229;class_code=**=;tss_id=TSS337;p_id=P1
>>>>
>>>>
>>>> due to the "class_code==" part (the value of the class code is
>>>> actually an equals sign). Obviously the bug occurs because "strsplit"
>>>> doesn't stop after the first split, but keeps splitting at subsequent
>>>> occurrences of the separator. I have modified the reader to be able to
>>>> handle this case, which as far as I know is perfectly valid. Instead
>>>> of strsplit, I use regexpr to find only the *first* occurrence of an
>>>> equals sign, and then I use substr to extract the part of the tag
>>>> before and after the equals sign. The attached file is a patch against
>>>> "R/gff.R" in the rtracklayer dist. I developed the patch against
>>>> version 1.16.1.
>>>>
>>>> Regards,
>>>>
>>>> -Ryan Thompson
>>>>
>>>>
>>>>
>>
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