v2.2.4

• Fixed a bug when some contigs of the reference genome are too small, smaller than the windowSize used in LRez to multi-thread the indexing (this caused a stoi error).
• Improved automatic recognition of Linked-read technology, allowing all technologies to have their barcode tag ending with "-1" (typically with haplotagging data mapped with the EMA mapper)

v2.2.3

• Fix bug with non gzipped fastq files indexing

• Add option "--collectionOfLists" to subcommand LRez query fastq to be able to give as input a FOF: e.g. a file containing files' names of lists of barcodes to search in the fastq file and the index (to perform LRez query fastq on multiple lists of barcodes, individually)

v2.2.2

• Fix bug with LRez stats when the total number of regions lower than the user-specified number of regions

v2.2.1

• Fix bug with gzipped fastq files indexing

v2.2

• Add a stats submodule to retrieve global statistics from BAM files
• Throw exceptions instead of exiting when encountering errors
• Add multithread support for all submodules

v2.1.3

• Fix bug with unmapped reads when comparing contigs extremities
• Add option to take as input a list of contigs to compare

v2.1.2

• Fix minor bug with SAM output

• Add an option to output SAM header when querying BAM files

v2.1.1

• Fix bug and skip indexation of reads that do not contain a BX:Z tag

v2.1

• Add support for the following linked-reads technologies:

  • 10x Genomics
  • Haplotagging
  • stLFR
  • TELL-Seq

• Index storage optimization

• Index the offsets of unaligned reads when using the index bam subcommand with option -f

• Add an option to extract duplicate barcodes when using the extract subcommand