Daniel C. Jones
Daniel C. Jones
I'll have a go at merging @luikore's changes. At a glance, it looks like it just adds features without breaking backwards compatibility, so it should be possible to have one...
The SIMD versions have to be specialized on 32 bit integers, but the generic implementation could be pretty easily made generic on coordinate type. It would be just be a...
Judging from your pull request, you figured this out already?
I think this is a pretty good plan! To my mind, getting testing and benchmarking squared away should probably be the priority. More comprehensive command line tools should probably be...
I'd be open to that change. It looks like @luikore has made a number of interesting additions I should think about merging.
Yes! The two biggest shortcomings with isolator are the rigidity of the model and difficultly scaling to large numbers of samples. I'm working on a new isoform quantification tool and...
Yeah, polee is the tool I was referencing here, thanks for noticing. It does more or less what I was trying to do with isolator, but can handle a very...
Thanks for the test case. It seems the old version of samtools included in isolator has no way to distinguish sam from bam and just segfaults if sam is opened...
You're correct, this should be fixed. It will end up using n^n threads during quantification I believe.
Yep! Add the `-v` option. E.g. ``` > quip -l h1-1_1.fastq.qp Reads Bases Uncompressed Compressed Ratio Filename 26516582 2651658200 6774592517 1080175349 0.1594 h1-1_1.fastq.qp ``` ``` > quip -l -v h1-1_1.fastq.qp...