v2.11.1: bugfixes

Update build_release.py

SPLASH 2.11.0

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)

SPLASH 2.3.0

Changelog:

• new parameter in splash allowing to choose n top target_entropy
• new software dsv_manip allows simple manipulation of delimiter-separated files (tsv, csv, etc.). Currently, it allows sorting the file by a given column and selecting only n records with the highest/lowest value of a given column.
• the number of threads for stages is now, by default, auto-configured but may still be overridden using appropriate parameters
• by default splash will also select 10k top target entropy anchors
• compactors: finding all anchors' occurrences in a read, not just the first one (--all_anchors switch),
• satc_merge: 2-mer and 3-mer sequence entropy for anchor and most frequent targets.

SPLASH 2.1.14

Compactors added

SPLASH 2.1.4

First release