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Hi --
I noticed the psl to bed script will not create separate entries for a split query-to-target hit in the PSL - it just takes the Tstart and Tend i.e. something with more than one blocks could be…
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bedops/bedmap/closest-features all have a broken --chrom option.
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If you merge bed to the continuous regions of overlapping or touching elements, the output reports only the reference start and end with no name - am I right? This is efficient and really makes sense …
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Consider file foo:
chr1 0 10
chr1 5 11
chr1 7 20
bedmap --count --bp-ovr 10 foo
gives the correct answer (1,0,1), while
bedmap --count --bp-ovr 10 --faster foo2
does not (1,1,1)
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Cf. http://bedops.uwencode.org/forum/index.php?topic=92.0 for details and possible test to reproduce issue
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There is a current scenario where bedmap will produce incorrect results.
foo1.bed:
chr1 1 200 a 1
chr1 10 20 b 3
chr1 50 150 c 4
foo2.bed:
chr1 1 200 a 1
Without --fa…
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Tests for nested element condition fail on this input:
```
chr1 1 2
chr1 2 10
chr1 2 12
chr1 4 12
chr1 4 12
chr1 10 30
chr2 30 40
chr2 30 50
chr2 35 40
chr2 …
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Add documentation for two new options and fix the description of how (literal) edge cases are handled per Vernot email thread.
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