must .bam files have their own line in my sampleAttribtes.txt file?

[Malcolm Cook]

Hi,

It appears now to me if I have two tracks with the same basename, say foo6.bam and foo6.bw, that I must have two lines in my sampleAttributes.txt file, one for each file, to have them recognized as being for the same "sample" and have their attributes identically color coded.

Like this:

DATAFILE    GENOTYPE    DOSE

foo6.bw        foo                 6

foo6.bam      foo                 6

I seem to remember that IGV would strip an extension (such as ".bam") from a filename to match it against or somehow no require me to duplicate this.

Am I mistaken?  Has IGV changed in this regard?  Am I missing a feature?  Is my best approach to use "Sample Mapping" and map both filenames to foo6, which would appear once in the sampleAttributes.txt?

Thanks!

~Malcolm

[Malcolm Cook]

Hello

A slight mistake on my part.  The extension of .bam does seem to not prevent a match with the value in column 1.  What I was observing was that the associate Junctions and Coverage tracks do NOT get colorized.  

I find that I can enable their coloration with the following:

#sampleMapping

foo6.bw Junctions\tfoo6.bw

foo6.bw Coverage\tfoo6.bw

So, perhaps this should be a feature  (bug fix?) request:

   Please make Junctions and Coverage .bam associated tracks receive the colors of their basename.

Thanks!

~Malcolm

[Malcolm Cook]

note: submitted to git as feature request: apply sample attributes automatically to more tracks #524