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1.10.0 (in progress)

1.0.9

  • Support dual UMI indexes with bamtag.

1.0.8

  • Add support for dual UMI indexes. Thanks @lbeltrame!

1.0.7

  • Ensure headers are not written when writing out a Series, to make us compatible with pandas > 0.24.
  • Fix for deprecated .ix call, .loc is the new replacement. Thanks to @naumenko-sa.

1.0.6

  • Fix for the python3 fix.

1.0.5

  • Fix for cb_filter with python3.

1.0.4

  • Enable cb_histogram to be used on samples without UMIs.
  • Enable filtering of cells during demultiplex_cells.
  • Fix incorrect pandas.read_csv call with header=-1.

1.0.3

  • Python 3 support

1.0.2

  • Add demultiplex_cells subcommand to break a transformed FASTQ file into separate FASTQ files by cell.
  • Future proofing for changes to panda's to_csv function.

1.0.1

  • Add support for click 7.0.

1.0.0

  • Fix for min-length filtering with paired samples. Previously required only one read to be longer, fix requires both.
  • Fix tests for fastqtagcount to use indexed BAM files.
  • Support gzipped cellular barcode files.
  • Support 10x V2 barcoding scheme. Thanks to @tomasgomes for the fix.
  • Re-enable streaming for cellular barcode filtering.
  • Add --umi_matrix option to fasttagcount. This outputs a non-umi-deduped matrix of counts, useful for QC.
  • Support gzipped files for sb_filter, mb_filter and add_uid.

0.8.0

  • Fix fasttagcount off-by-one issue.
  • Add version subcommand.
  • Fix missing pandas import in sparse subcommand.

0.7.0

  • Fix for kallisto output failing due to defaultdict not being imported. Thanks to @andreas-wilm for the fix.
  • Added tagcount option --parse_tags to use BAM tags rather than parsing read names (UM for UMI, CR for cell barcode)
  • Added tagcount option --gene_tags to use BAM tags to get ID of mapping gene (GX tag).
  • Fix tagcount with --genemap option not including a column name for the index.
  • Add sparse subcommand to turn a matrix into a sparse matrix.
  • Add fasttagcount subcommand. This assumes the input BAM/SAM file is coordinate sorted. Reduces memory usage by over 100x and runtime by 30-40% for deep samples.
  • Warn, don't fail if transcripts are missing from the genemap.

0.6.0

  • Fix skipping first piece of evidence when tagcounting.
  • Add test for tagcount.
  • Output full sorted transcript table from tagcount rather than only the observed transcripts.
  • Add --sparse option to output tagcount matrices in MatrixMarket format.
  • Allow cb_histogram subcommand to take gzipped files.
  • Allow cb_filter subcommand to take gzipped files.
  • Add support for triple-cellular barcodes.
  • Add example for Illumina SureCell (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/surecell-wta-ddseq.html)

0.5.0

  • Fix automatic format detection in cb_histogram.
  • Add tests for cb_histogram.
  • Re-enable streaming bamtagging. Thanks to @chapmanb for the suggestion.
  • Add subset_bamfile to subset a BAM file to keep alignments with a given set of cellular barcodes.
  • Speed improvements for reading gzipped FASTQ files.
  • Memory usage improvements for tagcount.

0.4.0

  • Fix for handling unicode, thanks to @chapmanb and @sowmyaiyer
  • Adds support for adding BAM tags to aligned fastqtransformed files. Thanks to @chapmanb.
  • Adds support for UMI-only fastqtransformation.
  • Adds support for paired-end target sequences.
  • Adds support for detecting sample barcodes via the SB tag in the regex.
  • Adds support for sample-based demultiplexing with error correction.

0.3.0

  • Now supports transforming 3-file input, as from the Linnarsson lab STRT-Seq data
  • New kallisto subcommand formats read files for input to kallisto's UMI mode
  • Fix gzip based fastq reading on Python 3.5
  • Including preliminary subcommand for guessing cell cutoff from cb_histogram

0.2.2

  • Added MANIFEST file which broke pip installation