v0.8.0

Buildable Source Tarball: smoothxg-v0.8.0.tar.gz

Full Changelog: v0.7.4...v0.8.0

v0.7.4

Buildable Source Tarball: smoothxg-v0.7.4.tar.gz

What's Changed

• fix odgi viz underflow by @AndreaGuarracino in #207

Full Changelog: v0.7.3...v0.7.4

v0.7.3

Buildable Source Tarball: smoothxg-v0.7.3.tar.gz

What's Changed

• update odgi by @AndreaGuarracino in #200
• update odgi by @AndreaGuarracino in #201
• update odgi by @AndreaGuarracino in #202
• update SPOA and abPOA by @AndreaGuarracino in #203
• update odgi by @AndreaGuarracino in #205
• Fix path embedding by @AndreaGuarracino in #206

Full Changelog: v0.7.2...v0.7.3

v0.7.2

Buildable Source Tarball: smoothxg-v0.7.2.tar.gz

What's Changed

• Avoid 2 graphs in memory, sample decompressed blocks, parallelize path embedding by @AndreaGuarracino in #197

Full Changelog: v0.7.1...v0.7.2

smoothxg 0.7.1 - Scoperto

Buildable Source Tarball: smoothxg-v0.7.1.tar.gz

The major news is a fix to avoid introducing links not supported by any path.

This introduces:

• fix uncovered edges #194 by @AndreaGuarracino
• small optimization and static build with GNU Guix #198 by @pjotrp
• less verbose logging and code cleaning #191 #196 by @AndreaGuarracino
• compatibility with GCC 13 #192 by @AndreaGuarracino
• update odgi and a bit more code cleaning #190 #193 #195 by @AndreaGuarracino

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

smoothxg 0.6.8 - Ciclico

Buildable Source Tarball: smoothxg-v0.6.8.tar.gz

This introduces:

• execute the smoothing multiple times #174 #176 by @AndreaGuarracino @subwaystation
• always emit long version format #175 by @AndreaGuarracino
• sync quantization parameters as in odgi sort #178 by @subwaystation
• update of odgi and new abPOA #180 by @AndreaGuarracino

smoothxg 0.6.7 - Sociale

Buildable Source Tarball: smoothxg-v0.6.7.tar.gz

This introduces:

• large fixed POA overlap #168 by @ekg
• Increase SPOA's portability (for Docker/Singularity) #169 by @AndreaGuarracino
• updated ODGI with faster sort and layout commands #170 by @AndreaGuarracino
• simplified versioning #172 by @AndreaGuarracino

citation release

For citation in the HPRC main paper.

smoothxg 0.6.5 - Locale

Buildable Source Tarball: smoothxg-v0.6.5.tar.gz

This introduces:

• temporary directory management (#160);
• local mode for the POA (#163);
• abPOA replaced by SPOA (#166);
• large fixed minimum overlap for the POA problems (#168).