0.11.3

Fix an issue on parsing feature barcode file with multiple modalities (PR #27 by @yihming )

0.11.2

Fix whitespace issue with Windows (PR #26 by @yihming )

0.11.1

Fix bug in ingesting reads (PR #25 by @bli25 )

0.11.0

This release contains the following changes (PR #24 by @bli25 ) :

• Add support on writing in BGZF format.
• Bug fix in izlib.h and improved error message.

0.10.0

Fastq file reading parser:

• Achieve faster multi-threaded fastq file reading by a simplified reimplementation of FQFeeder (PR #23 by @bli25 )

0.9.0

• Decompressing:
  • Use isa-l to replace zlib for faster decompression
  • Use slw287r's izlib.h as the interface to interact with kseq.h. (PR #20 PR #21 by @bli25 )
• Compressing:
  • Use libdeflate for faster compression
  • Add compress.hpp that enable single-threaded and multi-threaded compression (PR #22 by @bli25 )
• In input arguments:
  • Accept gzipped cell barcode file again
  • Add -p option for multi-threaded compression
• In output:
  • The sufficient statistics file is gzipped again, i.e.output_name.stat.csv.gz.

0.8.0

• On processing gzipped FASTQ files:
  • Remove boost library dependency.
  • Instead, use zlib and Heng Li's kseq library for fast I/O processing. (PR #17 by @tony-kuo ; PR #18 by @bli25 )
• In input arguments:
  • No longer accept gzipped cell barcode file, i.e. only .txt format is accepted.
• In output:
  • The sufficient statistics file output_name.stat.csv is no longer gzipped, but in .csv format.
  • Add output_name.report.txt to report statistics related to number of reads.

0.7.0

• Add --barcode-pos option for manually setting the barcode starting position (starting from 0) in Read 2.
• Add --convert-cell-barcode option to make the conversion of cell barcodes to match RNA cell barcodes for 10X data optional, so that other protocols such as CROP-Seq can still keep the original barcodes. Notice that for Hashing or CITE-Seq data, this option is automatically turned on for TotalSeq-B antibodies.
• Remove the obsolete --no-match-tso option.
• Bug fix in filter_chimeric_reads.

0.6.0

• Add --convert-cell-barcode option for converting cell barcode to match RNA cell barcodes for 10x Genomics' data.
• Bug fix in detecting totalA or totalBC chemistry.

0.5.0

Fix inconsistency issue with Pandas 1.2 when processing crispr data.