esvee v2.0

Functional:

• support for SBX and Ultima
• allow mismatches in line test ref bases
• prevent short local links in alignment interpretation for requeried alignments
• read ref base check matching seed multiple times requires non-low-base matches
• fixed min qual to test sequence comparisons
• ensure +/- orientation in assembly links for indels
• mark line reads only if ref base A/T repeats <= 20
• prep filter supps with low map qual (<10) and trimmed align length < 40
• require less than 1/3 bases as low-qual errors to add junction read, capture low-qual mismatches prior to consensus base determined
• fixed read parse state invalid, used by ref seq building
• add junction read check max repeat count diff
• soft-filter off-target variants

Technical:

• filter phase groups if assembly count exeeds 1k
• only support loading a single junction file