umis - v1.0.9

• Add fix for bamtag when using dual indexes.

- Python
Published by roryk over 3 years ago

umis - v1.0.8

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

- Python
Published by roryk almost 5 years ago

umis - v1.0.7

• 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.

- Python
Published by roryk over 6 years ago

umis - v1.0.6

Hotfix for encoding issues.

- Python
Published by roryk over 6 years ago

umis - v1.0.5

• Fix for cb_filter with python3. Thanks to @naumenko-sa for the fix.

- Python
Published by roryk over 6 years ago

umis - v1.0.4

• 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.

- Python
Published by roryk over 6 years ago

umis - v1.0.3

• Python 3 support

- Python
Published by roryk over 7 years ago

umis - v1.0.2

• 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.

- Python
Published by roryk over 7 years ago

umis - v1.0.1

1.0.1

• Add support for click 7.0.

- Python
Published by roryk almost 8 years ago

umis - 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.

- Python
Published by roryk about 8 years ago

umis - v0.8.0

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

- Python
Published by roryk almost 9 years ago

umis - v0.7.0

• 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.

- Python
Published by roryk almost 9 years ago

umis - v0.6.0

• 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)

- Python
Published by roryk about 9 years ago

umis - v0.5.0

• 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.

- Python
Published by roryk over 9 years ago

umis - BAM tagging and support for four file formats

• 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.

- Python
Published by roryk over 9 years ago

umis - 0.3

• 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

- Python
Published by vals almost 10 years ago

umis -

Changes since 0.2.1

• Added MANIFEST file which broke pip installation

- Python
Published by vals about 10 years ago