I added a feature to bowtie to directly generate BAM files*, and it seems to work well. If you think others could find this useful as well, I'd be happy to share the patches. Interested?
All the best
* For the R interface to bowtie I am currently working on, it is impractical to pipe bowtie's output to samtools to generate BAM files (and storing the intermediate SAM files is quite impractical due to their size).
Hi Thomas - yes, we'd love to see the patches. Please feel free to email them to me. It's not clear to me that this feature is needed, but if you've done the work I'd at least like to fold it in using #ifdefs to set it apart for now.
Why is it impractical to pipe bowtie's output to samtools in your scenario?
Well, I figured I'd be just as fast developing a BAMHitSink as I would be to figuring out how to make samtools and bowtie both part of the R-plugin-build-process and making the two of them comunicate with each other from inside R (as they should both run inside the R process, and not as separate processes). I haven't tried the later yet, but implementing the BAM output was pretty easy, anyways (To be fair, there is some functionality missing, e.g. -refout is not supported, since I didn't need that for my usecase. But if I'm not mistaken, SAM output doesn't support that either).
I'll send you the patches tomorrow, as soon as I figure out how to generate patch-files with SVN ;)
did you upload the patch? i was going to write it again until i saw this,
Hi there! The patches were never integrated into Bowtie, if I remember correctly I never heard back from Ben. Probably got caught in his spam filter or something :D
Anyways, if you need them, just tell me where to mail them :)
Hello Thomas -
I am interested in the patch. I am working with RHEL 5.4 and I have been running bowtie, converting the sam files to sorted bam files so that I can input the files in cufflinks. But every time I do I get an error from cufflinks. Using this patch could make this pipeline much easier to deal with.
Sorry for not responding sooner, I was on vacation. I wasn't sure what the best way to hand over the files was, so: this is the source for Bowtie 0.12.7 that contains my patch:
It includes everything you need (ie. bowtie source, the BamTools library I used and my own code), except for compiled binaries. But a simple 'make' should give you those as well. If you need the patch file itself, just diff the directory with the original bowtie-0.12.7 source.
I hope this is useful to you :) But please remember that I more or less hacked this together in my spare time, and for my own use-cases, so if anything doesn't work as expected or goes wrong, I am not to blame. You've been warned! :-p
That being said, let me know if you need any additional help ;)
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