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find_inserted_intervals large negative values #4

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kastman opened this issue Mar 21, 2018 · 0 comments
Open

find_inserted_intervals large negative values #4

kastman opened this issue Mar 21, 2018 · 0 comments

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@kastman
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kastman commented Mar 21, 2018

Occasionally with some alignments (currently in the non_ref_contigs.sh workflow) I'm getting very large negative numbers for the beginning of my intervals; e.g. https://github.com/yeastgenome/AGAPE/blob/master/non_ref_contigs.sh#L21

$BIN/find_inserted_intervals $out_dir/temp.maf $scf_name $len >> $out_dir/$seq_name.inserted.intervals

occasionally creates intervals like this (see unplaced-504 beginning at -536870911):

$ cat $seq_name.inserted.intervals | head 

unplaced-402 2 618
unplaced-423 485 1991
unplaced-504 -536870911 206
unplaced-529 1 1724
unplaced-563 1 1521

Any idea why this might be, and how to fix it?
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@kastman