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CHANGELOG.md

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Changelog

3.12.1

No user-facing changes

3.12.0

  • Update to Scala 3.3.1

3.11.0

  • Machine-parseable condition barcode summary file

3.10.0

  • More efficient and memory-safe sampling technique for unexpected sequence reporting

3.9.0

  • Use sampling technique for generating unexpected sequence reports

3.8.0

  • Replace kantan.csv with scala-csv

3.7.2

  • Parse barcodes from read IDs in demultiplexed mode

3.7.1

  • Adjust handling of command-line arguments in demultiplexed FASTQ file case

3.7.0

  • Support for processing demultiplexed FASTQ files

3.6.4

No user-facing changes

3.6.3

  • Documentation for processing demultiplexed FASTQ files

3.6.2

  • Additional validation of FASTQ records to detect badly concatenated files
  • Documentation for read ID check policy

3.6.1

  • Add a specialized template barcode policy to optimize a common use case, where a template matches 2 barcode regions, each of which has a short prefix, separated by a fixed length run of arbitrary barcodes.

3.6.0

  • Support reading multiple reads files sequentially as part of a single run

3.5.0

Released as open source under a BSD 3-Clause license

3.4.4

No user-facing changes

3.4.3

Improvements

  • Report empty conditions as "Unlabeled Sample Barcodes"

3.4.2

Improvements

  • Add support for different read ID checking policies, including one specific to Illumina which ignores divergent material after the first space in the ID line.

Bugfixes

  • Corrected fixed barcode prefix policies to allow the 'FIXED@' syntax, per the documentation; previous versions required the syntax 'FIXED:'. For backwards compatibility, the former syntax is still supported but in future versions this may be removed.

3.4.1

No user-facing changes

3.4.0

Improvements

  • Added support for reading row barcodes from paired-end sequencing data

3.3.4

Improvements

  • Improved error message in the case where reads are too short

3.3.3

No user-facing changes

3.3.2

No user-facing changes

3.3.1

Improvements

  • Advanced setting --always-count-col-barcodes (disabled by default). When enabled, PoolQ counts column barcodes from reads even if a row barcode is not found, which changes the per column barcode metrics Matched Sample Barcode and % Match, reported in the quality file.

3.3.0

Improvements

  • Support UMI barcodes

3.2.11

Improvements

  • Allow empty barcode IDs in row and column reference files

3.2.10

No user-facing changes

3.2.9

Improvements

  • Updated manual

3.2.8

No user-facing changes

3.2.7

No user-facing changes

3.2.6

No user-facing changes

3.2.5

No user-facing changes

3.2.4

No user-facing changes

3.2.3

Bugfixes

  • Correctly skip writing correlation file when there is only a single construct barcode or a single experimental condition

3.2.1

Improvements

  • Added whitespace to run info file for readability

3.2.0

Improvements

  • Add Normalized Match column to quality file
  • Change quality file header from Read counts for sample barcodes without associated conditions: to Read counts for most common sample barcodes without associated conditions:
  • Change terminology from scores to counts
  • Log version and run configuration in run info file
  • Add changelog

3.1.1

Bugfixes

  • Correctly skip writing correlation file when there is only a single experimental condition

3.1.0

No user-facing changes

3.0.5

Bugfixes

  • Fixed path to PoolQ jar in Makefile and scripts distributed with PoolQ

Improvements

  • Added regression tests for barcode counts and log-normalized counts files

3.0.4

Bugfixes

  • Fixed delimiter in Construct IDs field of log-normalized counts files

3.0.3

No user-facing changes

3.0.2

No user-facing changes

3.0.1

Improvements

  • Made 5' search limit optional when specifying a row barcode search template

3.0.0

  • Complete re-write of PoolQ