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Simple fixes needed in hsmerge.sh:
* Main body (bottom of file, currently line 143), need to add --sci to the bedmap command. Without it, FDR values below 1e-6 are erroneously being passed through…
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This is a feature request for closest-features. Would it be possible to add a switch to report upsteam or downstream features only? (when features overlap, the overlap should be reported as before). I…
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add weighted average option as requested by the community.
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For v2p4p21, need to also update mergeSort( ) for sort-bed, and bedops' --union option and the bed_check_iterator used by bedmap/bedextract/checkSort to adhere to the new sorting rules. Alex is worki…
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Given some sample input:
```
$ cat ~/test.h10.bed
chr1 192540940 192541170 CEL_rs1359062_1.28095631383106
chr1 192540940 192541170 MS_rs1359062_1.28095631383106
ch…
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bedmap incorrectly complains with --ec when numbers like 1.0e+3 are encountered.
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after the switch from bedmap's --count to --sum, I forgot to add in something that changes NAN to 0.
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Eric pointed out the following mistake on line 48 of density-peaks.bash:
bedmap --faster --sweep-all --chrom "$chr" --range "$rangepad" --delim "\t" --echo --echo-ref-row-id --count - "$tags"
--count…
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I compared the output of bedmap (version: 2.4.16) with map.bed and map.bed.starch:
`bedmap reference.bed map.bed.starch`
Output:
> 1 0 10000
> 1 10000 7047
> 1 20000 0
> 1 30000 0
> 1 40000 0
> 1 50…
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```
Demo link or sample code:
See the attached image. Here is a direct link to the same place:
http://bedmap.com/map?q=Park+at+38th%2C+New+York%2C+New+York%2C+United+States&z=
17
What steps will re…