Release notes

(For other release notes, see the individual releases that Bioconda pulls from, e.g. https://github.com/PacificBiosciences/pb-falcon/releases )

(Devs, see https://github.com/PacificBiosciences/pb-assembly/wiki/For-PB-devs )

Meta-packages

pb-assembly 0.0.8

• Latest
• Python3.7 only

pb-assembly 0.0.6

• Python3.6 and Python3.7!
• Python2.7 is no longer supported.
• pb-falcon >= 0.3.1

pb-assembly 0.0.5

• pb-falcon -> 0.2.7
• pbgcpp -> 0.0.1

pb-assembly 0.0.4

• pb-falcon -> 0.2.6
• An attempt to deal with the openssl problems in conda. No joy so far.
• See https://github.com/conda-forge/conda-forge.github.io/issues/701
• python-consensuscore2 -> 3.4.1 ("conda update -all" if needed)

pb-assembly 0.0.3

• pb-falcon -> 0.2.5
• htslib -> 1.9
• pbmm2 -> 0.12.0
• et al.

Packages

pb-falcon 2.2.4

pb-falcon 0.3.?

• falcon_kit
  • Use PYTHONHASHSEED for deterministic/reproducible dict-order.
  • Fix problem with gzip: https://github.com/PacificBiosciences/pbbioconda/issues/176
  • Use .fasta instead of .fa for all FASTA files. (falcon_unzip is also modified, for backwards compatibility.)

pb-falcon 0.3.4

• falcon_unzip
  • New resource request configuration.
  • Bug fix for filtered CCS reads not in DAZZ_DB that crash the phasing task.
• falcon_kit
  • Improved ovlp_filter, plus some bug-fixes.
  • Added zmw subsampling.

pb-falcon 0.3.3

• falcon_unzip
  • Import bug-fixes for the ccs assembly target

pb-falcon 0.3.2

• Add pysam dependency
• falcon_unzip
  • Stop checking for pbalign (since we normally use pbmm2)
  • Fix empty grep bug properly.
• falcon_kit
  • Fix use_subsampling

pb-falcon 0.3.1

• Python3.6 and Python3.7!
• Python2.7 is no longer supported.
• New experimental ccs target workflow.
• Fixes bugs in 0.3.0, which should not be used.

pb-falcon 0.2.7

(28 Feb 2019 -> 23 Apr 2019)

• Falcon_unzip 1.2.0
  • Use Gcpp instead of GenomicConsensus
• Falcon 1.3.0
• pypeFLOW 2.2.0

pb-falcon 0.2.6

(14 Jan 2019 -> 28 Feb 2019)

• Falcon_unzip 1.1.5
  • Use all subreads for polishing. (We used to use only 1 per zmw, same as assembly typically.)
    • Only if [Unzip]polish_include_zmw_all_subreads is "true".
  • The "IntervalTree" API has changed between versions, and no longer provides the search function. Unzip now handles both old and new API for fetching interval overlaps.
  • Use pbmm2 instead of blasr by default. ([Unzip]polish_use_blasr = true for blasr.)
• Falcon
  • Another fix for new msgpack in PyPI.

pb-falcon 0.2.5

(08 Oct 2018 -> 14 Jan 2019)

• Falcon
  • Added a threshold for repetitive k-mers in src/c/falcon.c (falcon-consensus). This prevents a combinatorial explosion in cases of very large low-complexity sequences.
  • Fixed DBdust user-settings propagation; added ovlp_DBdust_option, like pa_DBdust_option.
  • Always using -a for DBsplit; we now filter subreads before reads are in the Dazzler DB.
    • That filter now includes the streamed-longest option.
  • Stop calling time in bam2dexta.
    • This fixed a crash on some platforms.
• Falcon_unzip
  • Switch from pbalign (blasr) to pbmm2 (minimap2), by default, for alignment before variantCaller (arrow).
  • Stop ignoring errors in variantCaller, by default.
  • Fixed a crash: Exception: FATAL ERROR: Cycles in the graph?
    • Removed raising of an exception in case sketchy contigs are encountered from FALCON. It turns out that FALCON actually can generate those, which can break the execution. The raise was successful in catching this issue though, and now we know that we need to debug FALCON. However, instead of failing in Unzip, we will just log the problem, end return an empty list of regions. This will have an effect that all reads for this contig will be marked as unphased, and no haplotigs will be generated.
• Falcon-phase
  • Several bug-fixes; synced with Phase-Genomics upstream.
  • Added job.step sections for bwa/nucmer.
• Daligner suite
  • Synced with upstream repos (thegenemyers).