core region length in the elem file
Closed this issue · 2 comments
hrrsjeong commented
Hello! I found that many elements with the same element id have different (core) lengths. Below, I copied first 10 lines of the elem
file. As you can see, although 2nd and 3rd lines share the same core index of 1000_0
their length is very different. Also, I was wondering why the 6th column (core length) is not the same as 4th column - 3rd column +1
.
HG00733_hap1.masked h2tg000076l 3740761 3741639 1000_0 636 637 + CORE
HG00733_hap1.masked h2tg000085l 7729687 7730381 1000_0 357 140 - CORE
HG00733_hap1.masked h2tg000179l 1853817 1854097 1000_0 280 126 + CORE
HG00733_hap1.masked h2tg000076l 3741641 3742551 1000_1 450 450 +
HG00733_hap1.masked h2tg000179l 1854190 1854642 1000_1 377 87 +
HG00733_hap1.masked h2tg000017l 99364420 99366012 1002_0 1289 1286 - CORE
HG00733_hap1.masked h2tg000085l 5082532 5085049 1002_0 1217 158 + CORE
HG00733_hap1.masked h2tg000004l 85363675 85365239 1002_1 826 458 +
HG00733_hap1.masked h2tg000085l 4941770 4943670 1002_1 935 937 +
HG00733_hap1.masked h2tg000004l 85386073 85396709 1002_2 4768 1830 +
inumanag commented
Hi @hrrsjeong
Yeah, cores can have different lengths (e.g., 1000_0
in this case) due to the gaps/dissimilarities between core copies.
The sixth column should be the same... that is certainly a bug. Do you mind sharing the file that causes this problem (email is also OK)?
inumanag commented
Fixed in 1.3--- thank you for the report!