Re: [Bioc-devel] Slow performance on scanBam

2014-05-20 Thread James Bullard
Hi Martin, Thanks for the fix, I'll check it out. jim On Tue, May 20, 2014 at 12:35 PM, Martin Morgan wrote: > On 05/13/2014 08:17 AM, James Bullard wrote: > >> Hi Martin, thanks for the quick response. The data is certainly >> shareable. Here >> is a link to a bam + bai + sam file that I hav

Re: [Bioc-devel] Slow performance on scanBam

2014-05-20 Thread Martin Morgan
On 05/13/2014 08:17 AM, James Bullard wrote: Hi Martin, thanks for the quick response. The data is certainly shareable. Here is a link to a bam + bai + sam file that I have been using for benchmarking: https://www.dropbox.com/s/eat31mnmmco1zoh/example-bam.tar.bz2 There is a method in SAM to elid

Re: [Bioc-devel] Slow performance on scanBam

2014-05-13 Thread James Bullard
Hi Martin, thanks for the quick response. The data is certainly shareable. Here is a link to a bam + bai + sam file that I have been using for benchmarking: https://www.dropbox.com/s/eat31mnmmco1zoh/example-bam.tar.bz2 There is a method in SAM to elide the reference names from a header, but I thin

Re: [Bioc-devel] Slow performance on scanBam

2014-05-13 Thread Martin Morgan
Hi James -- I don't think there's anything in existence to make this easier, but I'll expose something in the next 24 hours; is your data shareable? There might be deeper things to be done for processing this small-but-numerous style data. Martin On 05/12/2014 05:32 PM, James Bullard wrote: I