Add information for all callers in INFO for overlapping events

[J35P312]

Hello @khurrammaqbool !

I have made so that svdb merge adds all stuff from INFO, SAMPLEs, and FILTER columns as discussed. Feel free to have a look ans test, I will merge once you are happy!

also added a bunch of tests

[codecov-commenter]

Codecov Report

Merging #48 (f01ed82) into master (8deb4e3) will increase coverage by 7.71%. The diff coverage is 40.22%.

@@            Coverage Diff             @@
##           master      #48      +/-   ##
==========================================
+ Coverage   10.61%   18.32%   +7.71%     
==========================================
  Files          10       10              
  Lines        1168     1233      +65     
==========================================
+ Hits          124      226     +102     
+ Misses       1044     1007      -37     

Flag	Coverage Δ
unittests	18.32% <40.22%> (+7.71%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
svdb/__main__.py	0.00% <0.00%> (ø)
svdb/merge_vcf_module.py	0.00% <0.00%> (ø)
svdb/merge_vcf_module_cython.py	19.39% <42.68%> (+19.39%)	:arrow_up:
svdb/overlap_module.py	89.28% <0.00%> (+17.85%)	:arrow_up:
svdb/readVCF.py	73.68% <0.00%> (+68.42%)	:arrow_up:

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[khurrammaqbool]

Thank you @J35P312! This looks better with sample and filter in addition to INFO. Below are few suggestions: CROM, POS, ID and QUAL added as separate items e.g. delly_CHR=1;delly_POS=123456;delly_ID=DUP00000067;delly_QUAL=960;.... adding ID will remove redundant entries of ID with INFO, FILTER and SAMPLE, if you agree to remove ID from these. Adding QUAL will make it possible to have to apply stringent downstream filtering after merging and/or perform comparisons.

[J35P312]

Thank you also! I have added delly_CHROM, delly_POS, delly_QUAL! I allso added svdb_origin tag, that lists the name of each input vcf (or tag); that way you will know the names of the tags. I have kept set as it is, it is modeled from gatk combine variants. Now I will merge this! thanks for testing =P.