smoothxg 0.7.0 - Deduplicato

Buildable Source Tarball: smoothxg-v0.7.0.tar.gz

Important: this version breaks backward compatibility, as the -S flag changes its meaning and becomes available only when smoothxg is compiled in debug mode (with the POA_DEBUG flag).

The main power-up in this version is the execution of partial order alignment (POA) on unique sequences by duplicating the POA blocks before their alignment. On average, the runtime improvement is around 5X with SPOA and abPOA; on nasty POA blocks, it can be >100X faster than before with SPOA.

This introduces:

• allow writing FASTAs of only hard blocks #181 by @AndreaGuarracino
• Perform the POA on unique sequences #183 by @AndreaGuarracino
• Run SPOA by default; the -S flag is replaced by -A to run abPOA #183 by @AndreaGuarracino
• Emit POA blocks information in a table #183 by @AndreaGuarracino
• Interface simplification: compile smoothxg with the POA_DEBUG flag to enable two debugging options (-S/--write-split-block-fastas and B/--write-poa-block-fastas) #183 by @AndreaGuarracino
• Fix versioning #186 by @AndreaGuarracino
• updated odgi with inject, paths, flip, overlap, and sort fixings #185 #187 #188 by @AndreaGuarracino