Debug Output Format

The debug output is a plaintext file with one line per filter:

• Read units aligned: total number of read pairs aligned to the library
• Units filtered due to being below score threshold: pairs that matched the reference, but were not above the score threshold set by score_threshold
• Units filtered due to multiple match: if discard_multiple_matches is on, the number of pairs that were discarded due to having more than one match
• Units filtered due to not matching the reference library and having a low score: pairs where one segment aligned, but with a score below score_threshold, and the other did not match
• Units filtered for different reasons between the forward and reverse read: pairs where both segments were filtered for disjoint reasons, except those covered by the previous line
• Units filtered due to a failed force intersect: if the intersect_level requires forced intersects and the intersection is completely disjoint, the pair will be filtered
• Units filtered due to mangled empty scores: pairs that weren't caught by the other filters, but did not match to the reference library
• Forward-running alignments discarded: the data is aligned twice -- once to a forward-running version of the library, and once to a reverse-running version. The better result is taken and the other direction's score discarded. These are the pairs/UMIs where a forward-running score was discarded.
• Reverse-running alignments discarded: pairs/UMIs where the reverse-running score was discarded
• Reverse-read sets discarded due to mangled paired-end data: if the UMIs are misaligned (odd number of entries per UMI), the entire reverse-read set will be discarded. This line logs the number of these discarded reads. This will be removed when this issue is resolved