CHANGELOG.md

Changelog

v4.0.0 (2023-10-04)

Feature

• V4 release (711ad95)

Breaking

• all TSV result headers are now PascalCase. --split-by-rg is now the default for strandedness and endedness. Percentages are now returned when 'Pct' is used in the header. strandedness now adds an overall entry when --split-by-rg. Read Groups are compared in the header definition and those found while sampling sequences. Discrepancies between the two are logged as an error. Header RGs without sequences are added as ZERO results to the output. endedness no longer exits with an ERROR on Unknown cases. (711ad95)

v3.4.0 (2023-10-04)

Feature

• V4 (#139) (33d9fb0)

v3.3.2 (2023-08-26)

Fix

• endedness: Missing key for dictionary (b077893)

v3.3.1 (2023-08-17)

Fix

• strandedness: Pass in required max_tries arg to main() (#136) (544be1a)

v3.3.0 (2023-08-16)

Feature

• Endedness subcommand (#124) (d61e82d)

Documentation

• encoding: n-samples -> n-reads (665d1d2)

v3.2.1 (2023-06-27)

Fix

• -1 n-reads default for encoding. don't falsely imply random sampling (#119) (c83275a)

v3.2.0 (2023-06-26)

Feature

• Handle case of BAM without RG tag (#100) (4436abf)

v3.1.1 (2023-05-08)

Fix

• Revert "feat: junction-saturation (#16)" (#110) (9262af0)

v3.1.0 (2023-03-23)

Feature

• Junction-saturation (#16) (e4811e7)

v3.0.0 (2023-03-22)

Feature

• junction-annotation: By default discard unannotated contigs (#96) (d2f2e18)
• Adds Dockerfile (#97) (26242b2)

Breaking

• Always annotate as unannotated_reference in the junctions file. By default, exclude from the summary report. With flag, call them "novel" in the summary (d2f2e18)

v2.3.1 (2023-02-22)

Fix

• Set default n-genes to 1000 for improved accuracy (914525d)

v2.3.0 (2023-02-21)

Feature

• Make retries cumulative instead of a reset (#91) (72c7b0f)

Documentation

• Clarify other important improvement regarding disambiguation of… (#15) (5d58156)
• Refactor to exclude junction-annotation from "best guess" notice (#13) (c8e208e)

v2.2.1 (2023-02-21)

Fix

• strandedness Make --max-iterations-per-try dynamic, based on --n-genes instead of a static default of 1000 (#88)

v2.2.0 (2021-06-24)

Feature

• instrument: Attempt to recover when read names not in Illumina format (#14) (9ab0951)

v2.1.0 (2021-04-05)

Feature

• Instead of failing on an unknown contig, try new gene (#11) (6ff35a5)

v2.0.0 (2021-03-11)

Fix

• Remove the option to override the default tab output delimiter (#12) (fbe382d)

Breaking

• This removes the --delimiter commandline arg (fbe382d)

v1.4.1 (2021-02-05)

Fix

• junction-annotation: Capitalize file in result outfile (fa01f8b)

v1.4.0 (2021-02-03)

Feature

• Junction annotation (#7) (f723731)

v1.3.0 (2021-02-02)

Feature

• Bam support for encoding (#9) (b1941a7)