v0.8.0

What's Changed

• Update unmap by @AroneyS in #18
  • renamed update
  • primarily for generating unmapped reads, running Aviary commands and/or downloading SRA reads
• Check for interleaved SRA by @AroneyS in #19
  • Account for interleaved and single-end reads from SRA (deinterleave and raise error, respectively)
• Add aligned fraction unmapping by @AroneyS in #20
  • Switch to using --min-read-percent-identity-pair and --min-read-aligned-percent-pair for CoverM unmapping
  • Default to 99% for both arguments

Full Changelog: v0.7.2...v0.8.0

v0.7.2

What's Changed

• Add taxa of interest filtering to query_processing by @AroneyS in #17

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

v0.7.1

Fix pypi uploading

Full Changelog: v0.7.0...v0.7.1

v0.7.0

What's Changed

• Remove S3.18.EIF_2_alpha sequences by @AroneyS in #15
• Account for nontarget unbinned sequences in evaluate script by @AroneyS in #16
• update unmapping max identity default to 99%

Full Changelog: v0.6.0...v0.7.0

v0.6.0

What's Changed

• Add argument to select specific coassemblies to unmap by @AroneyS in #11
• Switch from pandas to polars (much faster!) by @AroneyS in #12
• Add no-genomes argument for coassembly from scratch by @AroneyS in #14

Full Changelog: v0.5.1...v0.6.0

v0.5.1

What's Changed

• Add SRA-specific commands by @AroneyS in #3
  • Includes --sra argument to download SRA readsets
  • Includes --run-aviary to attempt to run aviary locally
  • Unable to implement properly due to snakemake/snakemake#1998, potentially fixed with snakemake/snakemake#1708. Aviary must be given as path to prebuilt conda env due to database setup requirements.

Full Changelog: v0.5.0...v0.5.1

v0.5.0

What's Changed

• Improve unmapping by @AroneyS in #8
• account for all clusters being filtered out by @AroneyS in #9
• Fix evaluate errors with multiple coassemblies by @AroneyS in #7
• Change name to Ibis by @AroneyS in #10

Full Changelog: v0.4.8...v0.5.0

v0.4.8

What's Changed

• Account for queried sequences returning no hits by @AroneyS in #4
• Create iterate subcommand by @AroneyS in #5
• Evaluate improvements by @AroneyS in #6

Full Changelog: v0.4.7...v0.4.8

v0.4.7

• Restrict SingleM in parallel by assuming each takes 8 threads (SingleM does not honor threads contract)
• Update SingleM to v1.0.0beta2
• Add -t CPUS argument to Aviary commands to enable rules to use more than 8 threads (default)

Full Changelog: v0.4.6...v0.4.7

v0.4.6

• Account for empty inputs at each stage
• Add more tests

Full Changelog: v0.4.5...v0.4.6