MatchIds

Using bench MatchId

MatchIds are used to tie base/comparison calls together. MatchIds have a structure of {chunkid}.{baseid}.{compid}. Where:

• chunkid - Unique id per-chunk of calls. All calls sharing chunkid were within --chunksize distance and were compared.
• baseid - The number of the base call from this chunk
• compid - The number of the comp call from this chunk

Doing basic pairing with MatchIds when results didn't have --multimatch is straight forward. For example, to tie tp-base.vcf and tp-comp.vcf calls together, they will have identical MatchIds.

MatchIds with _ for the baseid or compid are calls that were in a chunk without a counterpart (e.g. 5._.0 is the first comparison call from the fifth chunk, which had no base calls.)

Tieing a false positives/negatives to their closest matching counter part is a little tricker. For example, a false negative with MatchId 3.1.0, we'll need to look in both the fp.vcf and tp-comp.vcf for 3.*.0.

When using --multimatch there can be instances such as:

VCF         MatchId
tp-base     3.0.0
tp-comp     3.0.0
tp-comp     3.0.1

Here, the 0th base/comp call match to one another. Additionally, the 1st comp call 3.0.1 also matches to the 0th base call tp-base 3.0.0.