annotate for many fields per file

[jimhavrilla]

annotate can now take a comma separated list of field names, column numbers and operations for each file for score sets with multiple scores:

for example from a folder in the main directory:

python ../pathoscore.py annotate --scores ../score-sets/GRCh37/CCR/ccrs.autosomes.v2.20180420.bed.gz:CCR:4:max --scores ../score-sets/GRCh37/CCR/ccrs.xchrom.v2.20180420.bed.gz:CCR:4:max --scores ../score-sets/GRCh37/aloft/aloft.txt.gz:aloft_het,aloft_lof,aloft_rec:5,6,7:max,max,max --scores ../score-sets/GRCh37/fathmm/fathmm/fathmm.txt.gz:fathmm_non,fathmm_coding:5,6:max,max --scores ../score-sets/GRCh37/fitcons/fitcons/fitcons.bed.gz:fitCons:4:max ../truth-sets/GRCh37/clinvar/clinvar-benign.20170905.vcf.gz --prefix benign

this will make it so the user does not need to edit a conf file nor write the same file name many times.

[jimhavrilla]

I may want to add the example above to the README...

[jimhavrilla]

now the README has an example too.

[jimhavrilla]

@brentp is that better? I wrapped it like the example above it with visible backslashes

[jimhavrilla]

thanks for the advice!