Tags

Feature release "T. rex"

New features
* Support analysis of T cell receptor (TCR) sequences [note 1]
  [74dd84c, 4466259, eed9846, df525df, 3b5ef5e, de94039, b1fedb7,
  53c1a86, 4450917]

Enhancements
* Accelerate read mapping [eed9846]
* Accelerate quality control tag statistics [3b67562]
* Add support for 96x96 (9.0ki) matrix size [72e19a0]

Bugfixes
* Fix compatibility with new MySQL server mode [6ac6c8d, 3243025]
* Fix import of IgBLAST productivity status [70009cb]
* Fix parsing of IgBLAST region information [f6054e2]
* Fix import of metainformation table [4cdf8cd]
* Fix parsing of config file by spatials module [45e3a01]

Notes
[1] Currently only the analysis of TCR alpha/beta chain sequences
is supported, gamma/delta is still pending

Bugfix release, some enhancements

Bugfixes
- Fix use of regular expressions for CDR3 identification
- Fix insertion of IgBLAST score and E-values into the database
- Fix loss of sequences with long CDR3 and a mutated end-of-CDR3
  motif [note 1]
- Fix tag correction routine for large mouse matrix
- Fix handling of empty lines in metadata file

Enhancements
- More economic handling of database connections (includes time-outs)
- Remove unused (and unsafe) authentication options
- Add alternative CDR3 motifs to config
- Add script for repetitive testing of pipeline
- Further unification of log output

Notes
[1] Previous maximum length of CDR3 was 22 amino acids [aa],
otherwise the a assignment would fail if (and only if) an
alternative end-of-CDR3 motif was used by a sequence. This length
limit has now been extended (CDR3 plus J sequence 155 bp). Note
that IgBLAST currently (version 1.4.0) has a hard-coded maximum
V_end to J_start distance of 89 bp, which should constitute the
lower limit of the two.

Bugfix release, some minor enhancements

Bugfixes
* Fix instable makefile behavior [05c0b1d]
* Fix incompatibility with current RazorS version [f15a73c]
* Fix issues with concurrent data processing [fa76ec2]
* Fix path for metainfo tempate [6092a6d]
* Fix QC handling of missing locus [8c5f17c]
* Fix metadata table for Sanger sequences [18acb35]
* Fix pipeline_status query [4e0b654]
* Fix subregion identification for truncated sequences [e2d673e]
* Fix log blob overflow for Sanger metadata import [83a68a7]

Enhancements
* Adapt invocation of Sanger sequence processing to that of Matrix PCR data [18acb35]
* Add support for 72x64 (4.5ki) matrix size [2764486]
* Add log_level-aware logging for mutation identification module [92333f5]

first productive release