Problem with bedops starch
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3.3 years ago

I am having a problem with the starch statement, which is part of the bedops collection of functions. I am using bedops version 2.4.37

I have a simple, 1-line, tab delimited bedfile: "jctest.bed"

It looks like this

 somechrom 0 1 . 0

I can't display them here, but those 5 fields are delimited by tabs.

I turn that bed file into a starch file like this

 starch jctest.bed > jctest.starch

When I unstarch that file I get

 unstarch jctest.starch
 somechrom 0 1 . 0

That is expected behavior. But now I change "somechrom" to "somechrom.01", so jctest.bed now looks like this

 somechrom.01 0 1 . 0

I starch it, then unstarch it

 starch jctest.bed > jctest.starch
 unstarch jctest.starch
 somechrom 0 1 . 0

The ".01" suffix has disappeared ! This happens whenever a suffix of any kind, including character suffixes, is placed after a period in the chrom name field of the bed file.

Is this a known behavior? Intended? Seems undesirable.

starch bedops • 470 views
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