Skip to content

SPLASH 2.11.0
Compare
Choose a tag to compare
@marekkokot marekkokot released this 15 Oct 17:39
· 10 commits to master since this release
v2.11.0
220352b
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Learn about vigilant mode.

Changelog:

  • 10X/Visium input file support added (technical detail: it uses BKC on the first stage instead of KMC, and a number of extensions directly in splash code)

  • Lookup table added

  • Long reads support in compactors

  • MAC OS support

  • New column in output tsv file: pval_sample_spectral_sum

  • Default for --n_most_freq_targets is now 10 instead of 2; this may increase the file size noticeably

  • New parameters in splash:

    • --keep_significant_anchors_satc - additional output file containing SATC for significant anchors
    • --keep_top_target_entropy_anchors_satc - additional output file containing SATC for significant anchors with the highest target entropy

  • Compactors update: ability to test multiple extension candidates

    • --num_extenders <int> - number of extender candidates to be verified starting from the very end of the compactor (default: 1)
    • --extenders_shift <int> - shift in bases between extender candidates to be verified (default: 1)

  • Added new switches in compactors:

    • --no_subcompactors - do not include subcompactors in the output TSV (default: off)
    • --cumulated_stats - include columns with cumulated stats in the output TSV (default: off)
    • --independent_outputs - run compactors independently on a set of FASTQ files

  • Added new columns in the compactors output TSV:

    • id - compactor numerical identifier
    • parent_id - identifier of compactor's parent (-1 if no parent exists)
    • expected_read_count - expected number of compactor occurences in the reads,
    • cumulated_id - comma-separated list of identifiers of all compactor segments (only with --cumulated_stats flag),
    • cumulated_exact_support - comma-separated list of exact_support of all compactor segments (only with --cumulated_stats flag),
    • cumulated_extender_specificity - comma-separated list of extender_specificity of all compactor segments (only with --cumulated_stats flag).

  • new flag --keep_top_n_effect_size_bin, with a default value of 20k - it is similar to --keep_top_n_target_entropy, but select anchors with top effect size bin.

  • new flag --keep_top_effect_size_bin_anchors_satc - similar to --keep_top_target_entropy_anchors_satc but for top effect size bin, i.e., it creates an additional output file containing SATC for significant anchors with the top effect size bin. The additional output file is in SATC binary format and may be dumped to text with satc_dump.

  • various bugfixes

  • various optimizations

  • small change in satc file format (ordering of record parts added)

Assets 6
Loading