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maf genome position #6

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AlisaGU opened this issue Oct 31, 2022 · 1 comment
Open

maf genome position #6

AlisaGU opened this issue Oct 31, 2022 · 1 comment

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@AlisaGU
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AlisaGU commented Oct 31, 2022

Hi, thanks for providing this useful tool.
It seems a small bug in genome position of maf

##maf version=1 
a score=262.0
s Xenopus_tropicalis.chr5           29721 13 + 164033575 CCCCCCGTTTGTT
s Ambystoma_mexicana.chr8q      150634379 13 + 886375962 TAATTCCTTTCTC
s Andrias_davidianus.ptg000471l   1972369 13 +   2026336 CCTTCTGCTTTCC
s Hynobius_yiwuensis.Contig128   31709499 13 -  45235456 CTTTTTAATTTCC

The corresponding result is
image

For example, the genomic position of Xenopus tropicalis should be 29722~29734 (13 bp).

@thomasabeel
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I think the display values are simply calculated as start (29722) plus the length (13), which would yield 29735. Depending whether you interpret the ranges to be inclusive (29722-29734) or right-exclusive (29722-29735), both your proposed range and the currently displayed value would be correct. I'm leaving the ticket open for now.

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