bedtools version 2.22.0

Enhancements

1. Multiple database support for the closest tool. The closest tool now requires sorted input, but it is between 10 and 60 times faster depending on the use case.

As an example:

➜  cat mq1.bed
chr1    80  100 q1  1   +

➜  cat mdb1.bed
chr1    5   15  d1.1    1   +
chr1    20  60  d1.2    2   -
chr1    200 220 d1.3    3   -

➜  cat mdb2.bed
chr1    15  35  db2.1   1   -
chr1    120 170 db2.2   2   -
chr1    210 230 db3 3   +

➜  cat mdb3.bed
chr1    70  90  d3.1    3   -

Find the closest interval in each B file.

➜  bedtools closest -a mq1.bed \
          -b mdb1.bed mdb2.bed mdb3.bed \
          -names foo bar biz
chr1    80  100 q1  1   +   foo chr1    20  60  d1.2    2   -
chr1    80  100 q1  1   +   bar chr1    120 170 db2.2   2   -
chr1    80  100 q1  1   +   biz chr1    70  90  d3.1    3   -

Find the closest interval among all B files.

➜  bedtools closest -a mq1.bed \
         -b mdb1.bed mdb2.bed mdb3.bed \
         -names foo bar biz \
         -mdb all
chr1    80  100 q1  1   +   biz chr1    70  90  d3.1    3   -

1. Support for IMPRECISE SVs in VCF format.
2. Added the -prec option to grouby to allow control over the reported decimal precision

Bug fixes

1. Fixed a bug with zero length records.
2. Fixed a precision bug in the fisher tool. Thanks to @brentp
3. Fixed a bug in the bamtofastq tool. Thanks to @ryan-williams