bedops
bedops copied to clipboard
Investigate having `--min`/`--max`/etc. operators support `--echo-*` with `--prec N`
Given A.bed
:
chr1 2849089 2849142 id-639 35 . -1 -1 3.51493
Given B.bed
:
chr1 2849089 2849124 i 0.000838724
chr1 2849124 2849125 i 0.000305542
chr1 2849125 2849132 i 0.000428122
chr1 2849132 2849134 i 0.000600718
chr1 2849134 2849142 i 0.000428122
Consider output from this command:
$ bedmap --chrom chr1 --sci --prec 5 --echo --echo-map --min --min-element A.bed B.bed
chr1 2849089 2849142 id-639 35 . -1 -1 3.51493|chr1 2849089 2849124 i 0.000839;chr1 2849124 2849125 i 0.000306;chr1 2849125 2849132 i 0.000428;chr1 2849132 2849134 i 0.000601;chr1 2849134 2849142 i 0.000428|3.05542e-04|chr1 2849124 2849125 i 3.05542e-04
While --min
and --min-element
use --sci --prec 5
to report the score value of the minimum-scoring element with the specified precision, --echo
and --echo-map
do not.
It might be worth taking a look at the patches leading up to v2.4.12 to see what would be involved in reformatting score output from --echo-*
operations.
Perhaps a --apply-prec-to-all
or similar option could be used to preserve existing behavior for older pipelines. Or we break with the old approach and apply the format specifier globally, if specified via --prec
.
A related issue may be #219. Performance concerns were raised by Shane.