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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<- )
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
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?
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?
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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?
>
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> 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>
> .
>
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.
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mskilab commentedon Mar 20, 2016
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 commentedon Dec 5, 2016
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 commentedon Dec 6, 2016
mskilab commentedon Dec 6, 2016
KhagayN commentedon Dec 6, 2016
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.