Hi Martin and Hervé ,

Thank you so much for the updates and response to those requests, I am
looking forward to the new features and next release of those packages.

Cheers,

Tengfei

2011/8/10 Hervé Pagès <hpages@fhcrc.org>

> Thanks Tengfei and Cory for the feedback. Those requests make
> a lot of sense and we agree that the GappedAlignments container
> will benefit a lot from this kind of improvements. We'll do our
> best to implement most of them in one way or another before the
> next release.
>
> Cheers,
> H.
>
>
>
> On 11-08-09 01:50 PM, Martin Morgan wrote:
>
>> On 08/09/2011 11:58 AM, Cory Barr wrote:
>>
>>> I would find being able to pass the "what" component of a ScanBamParam
>>> object to readBamGappedAlignments very helpful. Like Tengfei, I often
>>> read
>>> in a BAM file from readBamGappedAlignments and also scanBam then
>>> combine the
>>> information.
>>>
>>
>> As a start, GappedAlignments() in 1.5.23 has a new ... argument used to
>> populate elementMetadata. So e.g.,
>>
>> bam <- scanBam(<...>)
>> with(bam[[1]], GappedAlignments(<...>, qual=qual))
>>
>> Martin
>>
>>  Being able to maintain information on a read's mate via
>>> readBamGappedAlignments would also get much use from me. Currently, to do
>>> this I combine information from scanBam, parse out the end number from
>>> the
>>> BAM flag, and then regroup a GRangesList to include its mate. Doing this
>>> efficiently by passing an argument to grglist would be great.
>>>
>>> -Cory
>>>
>>> On Tue, Aug 9, 2011 at 11:33 AM, Tengfei Yin<yintengfei@gmail.com>
>>> wrote:
>>>
>>>  Dear all,
>>>>
>>>> I am using GenomicRanges and Rsamtools a lot for my work, they are
>>>> extremely
>>>> helpful and neat packages to deal with NGS data, thanks a lot for those
>>>> people how contribute to all those nice packages in BioC. I just have
>>>> some
>>>> features request for the GappedAlignments, probably it's already
>>>> there or
>>>> it's not a good practice to do it in certain way, please feel free to
>>>> let
>>>> me
>>>> know.
>>>>
>>>> I like features from both scanBam or readBamGappedAlignments, just
>>>> sometime
>>>> I need to write my own script trying to combine information from
>>>> those two
>>>> function and make a "general" granges to work with. So I am wondering if
>>>> there is any way to do it in a neat way or is there a plan to implement
>>>> similiar features?
>>>>
>>>> - Including more element meta data with GappedAlignments
>>>> - there is "which" in readBamGappedAlignments, can I have some thing
>>>> like "param" or "what" to get more info from bam file and associate
>>>> them
>>>> with Gapped reads.
>>>> - When doing the coerce from GappedAlignement to GRanges, or call
>>>> granges() on GappedAlignments object, it only return the minimal
>>>> information, "qwidth", "cigar", "ngap" is not included as
>>>> elementMetadata.
>>>> - Including more pairing information for pair-end RNA-seq
>>>> - So I could know the mated information with certain gapped reads,
>>>> either plot it as pair-end read or do some computation on it.
>>>> - Setting flags for each entry, so I can filter it out based on the
>>>> flags, something like from scanBamFlag?
>>>> - grglist to transform the data in different way
>>>>
>>>> If I can get a general data structure which combine all those
>>>> information
>>>> and or features together, that would be nice, I realize it's hard to
>>>> combine all information together and make it flexible at the same time ,
>>>> e.g. you need to deal with how to binding element meta data for paired
>>>> entry, probably showing seq1/seq2 to indicate which sequence it's
>>>> belongs
>>>> too? how to handle multiple hits?
>>>>
>>>> Right now, I am making my own "giant" GRanges object which including all
>>>> the
>>>> information I want, but that's too specific for my work, that's why I am
>>>> wondering if there is any plan to combine those neat features
>>>> together and
>>>> bring a more flexible data structure.
>>>>
>>>> Thanks!
>>>>
>>>> Tengfei
>>>>
>>>>
>>>> --
>>>> Tengfei Yin
>>>> MCDB PhD student
>>>> 1620 Howe Hall, 2274,
>>>> Iowa State University
>>>> Ames, IA,50011-2274
>>>> Homepage: www.tengfei.name
>>>>
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>>
>>
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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>



-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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