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CHANGELOG.md

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preprocess16S changelog

2024-09-27 edition.

Version changes:

  • Fixed a bug (a single bloody missed comma!) that would not allow preprocess16S to parse option --primers.

5.0.g -> 5.0.h

2021-05-06 edition.

  • Switched the default -x value to 0.60, and the default -s value to 3. These values show the best results when detecting standard Illumina V3-V4 primer sequences, namely: precision -- 0.983, recall -- 0.994, F-measure -- 0.988. Here, I consider "positive" result of such a classification as identification of a non-crosstalk read, and identification of a crosstalk read -- as "negative" result.

Version changes:

5.0.f -> 5.0.g

2021-02-24 edition.

  • Fixed bug that would cause preprocess16S to crash if it's output is redirected somewhere, e.g. with tee.

Version changes:

5.0.e -> 5.0.f

2021-02-23 edition.

  • preprocess16S now saves command with which it was run to log file.

Version changes:

5.0.d -> 5.0.e

2021-02-21 edition.

  • fixed bug that would cause preprocess16S not to print error message if NGmerge binary file is not executable.

Version changes:

5.0.c -> 5.0.d

2021-02-20 evening edition.

  • fixed bug that would cause preprocess16S to ignore option -o.

Version changes:

5.0.b -> 5.0.c

2021-02-20 edition.

  • preprocess16S now checks it "forward" and "reverse" files are actually different files.
  • Small bug fix.

Version changes:

5.0.a -> 5.0.b

2021-02-18 edition.

A major revision was done.

  • Maximum offset and threshold values in crosstalk detection can now be defined by user.
  • Removed reference-guided merging of non-overlapping reads until better time.
  • Removed creation of quality plot (it is by no means necessary here).
  • Changed names of some options.

Version changes:

4.0.d -> 5.0.a

2020-12-16 edition.

Flag --fill-gaps is replaced with --no-ovlp-merge with the same functionality. The reason is that users used to have hard time understanding it's description in README.md, and inappropriate name of the flag just exacerbated the frustration.

Version changes:

  • preprocess16S: 4.0.c --> 4.0.d
  • read_mering_16S: 4.0.d --> 4.0.c

2020-10-23 edition. Version 4.0.c

  1. Fixed bug that would cause preprocess16S to write "primers were not trimmed" to log if primers actually WERE trimmed.

2020-07-14 edition. Version 4.0.b

  1. Fixed bug that would cause scripts to terminate execution if BLAST+ is not installed, but --fill-gaps is not specified.

2020-07-13 edition. Version 4.0.a

  1. First smerging step is replaced with NGmerge program.
  2. Second merging step is improved: it now uses information from alignment of reverse read if alignment of forward read is ambiguous.
  3. NGmerge's quality profile is adopted.

Unfortunately, changes were not tracked in this way before 2020-07-13.