Version-1.02.5

Fixed one-off bug in #63 when applied to empty or chimeric reads.

Version-1.02.4

This is a minor release which fixes two bugs:

• #63 "One-off" bug in trimming
• #61 Empty read causing segfault

Version-1.02.3

What's Changed

• Fix flexiplex_filter bug caused by small barcode lists
• Fix out_of_range error in substr
• Add a flag to report chimeric reads
• Add CB UB tag to fastq id field
• Update flexiplex-filter to work on newer Python versions (and Numpy version update)
• Overwrite old stats file instead of appending
• Small fixes

Full Changelog: v1.01...v1.02.3

Version-1.01

Major new release:

What has changed?

• More flexible barcode structures can now be specified: -x for each flanking sequence, -b for barcode pattern, -u for UMI pattern), where the order now matters. e.g. 10x style barcodes can be given as -x [left flank] -b [barcode pattern] -u [umi pattern] -x [right flank], but complex patterns are now allowed such as -x [left flank] -u [umi pattern] -x [middle flank] -b [barcode pattern] -x [right flank]. Flanking sequence and patterns can include wildcards "?" and IUPAC codes.
• Predefined settings for the common use cases of 10x 3' v3, 10x 3' v2, 10x 5' v2 and grep have been implemented. Requests to expand these are very welcome.
• Further development of flexiplex-filter for automatically estimating the number of cells/barcodes in an experiment and generating a short-list of barcodes.
• Note: This version is not backwards compatible and will likely break scripts developed with older versions. Importantly, the order of command line options now matters.

What has not changed?

• Performance metrics such as searching/demultiplexing sensitivity and specificity, computational speed and memory utilisation remain very similar to the previous version.

Version-0.97.1

This minor release makes it easier to install and use flexiplex and has no changes to existing functionality. By using make install, it is now possible to install both flexiplex and flexiplex-filter.

Version-0.97

Bumps version, removes extra tab in output table, updates binaries