chr.sub

[walaj]

Propose removing this. Not sure what the issue is with having "chr" in the seqinfo, and it seems like if there is a problem, a more general solution should be used (e.g. manipulate seqinfo however you like on your own, and then set with seqinfo<- )

[mskilab]

sure agree in principle

this basically applies to gTrack that we build off external files - e.g. .bam, .wig., .bw etc where you can't manipulate the seqinfo in that manner

in practice "chr" are a <> since a lot of UCSC tracks will be stored as .bw with chr prefixes and then you're trying to plot them against your broad .bam which has no "chr" ...

open to other fixes .. but we should have a solution for this

[KhagayN]

if chr.sub is removed, how would we remove the "chr" prefixes from external files such as .bam, .wig, .bw where they can't be manipulated by using the seqinfo function?

[mskilab]

agree w Khagay - this is a very common problem for UCSC vs other files in practice not very elegant of course, but in practice would be a huge PITA to get rid of since about half of bw / bam / wig data use the "chr" designation and then the data become incomparable to each other and granges that we use in house ..

…

On Mon, Dec 5, 2016 at 3:16 PM, Khagay Nagdimov ***@***.***> wrote: if chr.sub is removed, how would we remove the "chr" prefixes from external files such as .bam, .wig, .bw where they can't be manipulated by using the seqinfo function? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AL-0kRolgDXKaMG2VNAycd6i-y0e0piYks5rFHEJgaJpZM4H0xaX> .

[mskilab]

though I have seen situations where this behaves unexpectedly so might need some debugging .. not sure if this is what JW is referring to On Tue, Dec 6, 2016 at 11:02 AM, Marcin Imielinski < marcin.imielinski@gmail.com> wrote:

…

agree w Khagay - this is a very common problem for UCSC vs other files in practice not very elegant of course, but in practice would be a huge PITA to get rid of since about half of bw / bam / wig data use the "chr" designation and then the data become incomparable to each other and granges that we use in house .. On Mon, Dec 5, 2016 at 3:16 PM, Khagay Nagdimov ***@***.***> wrote: > if chr.sub is removed, how would we remove the "chr" prefixes from > external files such as .bam, .wig, .bw where they can't be manipulated by > using the seqinfo function? > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#4 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AL-0kRolgDXKaMG2VNAycd6i-y0e0piYks5rFHEJgaJpZM4H0xaX> > . >

[KhagayN]

ahh, especially as you mentioned on Mar 20, when plotting these tracks against broad .bam that has no "chr". Sounds like keeping chr.sub is a good idea but, include tests that chr.sub works for the external files that can be inputted.