[BioC] export a GappedAlignment object to a BAM file

[Martin Morgan]

On 05/08/2012 07:07 AM, Yue Li wrote:
> Hi Michael,
>
> Sure. I am working on it and will let you know once it is ready. Basically, we need a function (e.g. exportGappedAlignments) or an inheritance method something like export.GappedAlignments to export the objects of that class, right?

GappedAlignments doesn't really contain enough information for an 
informative BAM file, e.g., reads, qualities, alignment scores, ... Also 
presumably header information in the original BAM would need to be 
carried forward... Not that I have anything better to offer (other than 
filterBam for simple filtering of reads).

Martin

> Thanks,
> Yue
>
> On 2012-05-08, at 9:37 AM, Michael Lawrence wrote:
>
>> Good point. We should add GappedAlignments export to BAM into rtracklayer. I recently added BAM import to devel. Without any help from Rsamtools though, we would need to use the strategy that you outline: write out a SAM file and asBam() it. That's not so bad though. Do you think you could submit this as a patch?
>>
>> Thanks,
>> Michael
>>
>> On Tue, May 8, 2012 at 6:24 AM, Yue Li<gorillayue at gmail.com>  wrote:
>> Dear List,
>>
>> I wonder if there's a way to export a GappedAlignment object to a bam file.
>>
>> rtracklayer 'export' function exports gff, bed, bed15, bedGraph but not bam. It also does not recognize GappedAlignment class.
>>
>> One could reformat the GappedAlignment object into a SAM-like table, write.table it to a local disk, and then use 'asBAM' to convert that file to BAM. But that seems a little cumbersome.
>>
>> Thanks much,
>> Yue
>>
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