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2021-12-17biology/vsearch: Update to 2.18.0bacon7-32/+42
Add powerpc64 support Numerous fixes and enhancements since 2.13 Changes: https://github.com/torognes/vsearch/tags
2021-12-17biology/cdhit: Update to 4.8.1bacon3-15/+21
Add support for gzipped input Changes: https://github.com/weizhongli/cdhit/releases
2021-12-17biology/bowtie2: Update to 2.4.4bacon5-20/+14
Replaced TBB with C++ threads Support for Apple M1 Several other fixes and enhancements Changes: https://github.com/BenLangmead/bowtie2/tags
2021-12-17biology/bcftools: Update to 1.14bacon4-10/+8
Numerous fixes and enhancments since 1.12 Changes: https://github.com/samtools/bcftools/tags
2021-12-17biology/samtools: Update to 1.14bacon4-10/+10
Numerous fixes and enhancements since 1.12 Changes: https://github.com/samtools/samtools/tags
2021-12-17biology/htslib: Update to 1.14bacon4-11/+10
Numerous fixes and enhancements since 1.12 Changes: https://github.com/samtools/htslib/releases/tag/1.14
2021-12-14biology/vcf2hap: Update to 0.1.4bacon3-9/+9
Updates for evolving libxtend and biolibc APIs Add --version flag
2021-12-14biology/vcf-split: Update to 0.1.3.3bacon3-9/+10
Transfer header from multi-sample input Updates for evolving libxtend and biolibc APIs Add --version flag Numerous minor fixes and enhancements
2021-12-14biology/peak-classifier: Update to 0.1.2bacon3-9/+7
Mainly updates for evolving libxtend and biolibc APIs A few minor fixes and enhancements
2021-12-14biology/biolibc-tools: Update to 0.1.1bacon3-15/+31
Make all programs subcommands of "blt" Several new commands Updates for evolving libxtend and biolibc APIs Add --version flag Numerous minor fixes and enhancements Changes: https://github.com/auerlab/biolibc-tools/releases/tag/0.1.1
2021-12-14biology/ad2vcf: Update to 0.1.4bacon3-9/+9
Updates for evolving libxtend and biolibc APIs Add --version flag Filter out unused SAM fields on input Numerous other minor fixes and enhancements Changes: https://github.com/auerlab/ad2vcf/releases/tag/0.1.4
2021-12-14biology/biolibc: Update to 0.2.1bacon5-337/+158
Add orf.c with start/stop codon locators Standardize BED and GFF APIs Implement VCF input filtering Eliminate mutator macros mirroring mutator functions Numerous minor bug fixes and enhancements Changes: https://github.com/auerlab/biolibc/releases/tag/0.2.1
2021-12-08revbump for icu and libffiadam12-24/+24
2021-11-11*: Revbump for protobuf-3.19.0kim1-2/+2
Fix for: Shared object "libprotobuf.so.29" not found
2021-10-26biology: Replace RMD160 checksums with BLAKE2s checksumsnia73-150/+150
All checksums have been double-checked against existing RMD160 and SHA512 hashes
2021-10-21*: Revbump for protobuf-3.18.0kim1-2/+2
Fix for: Shared object "libprotobuf.so.28" not found
2021-10-07biology: Remove SHA1 hashes for distfilesnia73-150/+73
2021-10-04py-pydicom: updated to 2.2.2adam2-7/+7
Version 2.2.0 Changes ------- * Data elements with a VR of **AT** must now be set with values acceptable to :func:`~pydicom.tag.Tag`, and are always stored as a :class:`~pydicom.tag.BaseTag`. Previously, any Python type could be set. * :meth:`BaseTag.__eq__()<pydicom.tag.BaseTag.__eq__>` returns ``False`` rather than raising an exception when the operand cannot be converted to :class:`~pydicom.tag.BaseTag` (:pr:`1327`) * :meth:`DA.__str__()<pydicom.valuerep.DA.__str__>`, :meth:`DT.__str__()<pydicom.valuerep.DT.__str__>` and :meth:`TM.__str__()<pydicom.valuerep.TM.__str__>` return valid DICOM strings instead of the formatted date and time representations (:issue:`1262`) * If comparing :class:`~pydicom.dataset.FileDataset` instances, the file metadata is now ignored. This makes it possible to compare a :class:`~pydicom.dataset.FileDataset` object with a :class:`~pydicom.dataset.Dataset` object. * :func:`~pydicom.pixel_data_handlers.rle_handler.rle_encode_frame` is deprecated and will be removed in v3.0, use :meth:`~pydicom.dataset.Dataset.compress` or :attr:`~pydicom.encoders.RLELosslessEncoder` instead. * :func:`~pydicom.filereader.read_file` is deprecated and will be removed in v3.0, use :func:`~pydicom.filereader.dcmread` instead. * :func:`~pydicom.filewriter.write_file` is deprecated and will be removed in v3.0, use :func:`~pydicom.filewriter.dcmwrite` instead. * Data dictionaries updated to version 2021b of the DICOM Standard * :class:`~pydicom.dataset.Dataset` no longer inherits from :class:`dict` Enhancements ------------ * Added a command-line interface for pydicom. Current subcommands are: * ``show``: display all or part of a DICOM file * ``codify`` to produce Python code for writing files or sequence items from scratch. Please see the :ref:`cli_guide` for examples and details of all the options for each command. * A field containing an invalid number of bytes will result in a warning instead of an exception when :attr:`~pydicom.config.convert_wrong_length_to_UN` is set to ``True``. * Private tags known via the private dictionary will now get the configured VR if read from a dataset instead of **UN** (:issue:`1051`). * While reading explicit VR, a switch to implicit VR will be silently attempted if the VR bytes are not valid VR characters, and config option :attr:`~pydicom.config.assume_implicit_vr_switch` is ``True`` (default) * New functionality to help with correct formatting of decimal strings (**DS**) * Added :func:`~pydicom.valuerep.is_valid_ds` to check whether a string is valid as a DICOM decimal string and :func:`~pydicom.valuerep.format_number_as_ds` to format a given ``float`` or ``Decimal`` as a DS while retaining the highest possible level of precision * If :attr:`~pydicom.config.enforce_valid_values` is set to ``True``, all **DS** objects created will be checked for the validity of their string representations. * Added optional ``auto_format`` parameter to the init methods of :class:`~pydicom.valuerep.DSfloat` and :class:`~pydicom.valuerep.DSdecimal` and the :func:`~pydicom.valuerep.DS` factory function to allow explicitly requesting automatic formatting of the string representations of these objects when they are constructed. * Added methods to construct :class:`~pydicom.valuerep.PersonName` objects from individual components of names (``family_name``, ``given_name``, etc.). See :meth:`~pydicom.valuerep.PersonName.from_named_components` and :meth:`~pydicom.valuerep.PersonName.from_named_components_veterinary`. * Added support for downloading the large test files with the `requests <https://docs.python-requests.org/en/master/>`_ package in addition to :mod:`urllib.request` (:pr:`1340`) * Ensured :func:`~pydicom.pixel_data_handlers.util.convert_color_space` uses 32-bit floats for calculation, added `per_frame` flag to allow frame-by-frame processing and improved the speed by ~20-60% (:issue:`1348`) * Optimisations for RLE encoding using *pydicom* (~40% faster). * Added support for faster decoding (~4-5x) and encoding (~20x) of *RLE Lossless* *Pixel Data* via the `pylibjpeg-rle <https://github.com/pydicom/pylibjpeg-rle>`_ plugin (:pr:`1361`, :pr:`1372`). * Added :func:`Dataset.compress()<pydicom.dataset.Dataset.compress>` function for compressing uncompressed pixel data using a given encoding format as specified by a UID. Only *RLE Lossless* is currently supported (:pr:`1372`) * Added :mod:`~pydicom.encoders` module and the following encoders: * :attr:`~pydicom.encoders.RLELosslessEncoder` with 'pydicom', 'pylibjpeg' and 'gdcm' plugins * Added `read` parameter to :func:`~pydicom.data.get_testdata_file` to allow reading and returning the corresponding dataset (:pr:`1372`) * Handle decoded RLE segments with padding (:issue:`1438`) * Add option to JSON functions to suppress exception and continue (:pr:`1332`) * Allow searching :class:`~pydicom.fileset.FileSet` s for a list of elements (:pr:`1428`) * Added hash function to SR :class:`~pydicom.sr.Code` (:pr:`1434`) Fixes ----- * Fixed pickling a :class:`~pydicom.dataset.Dataset` instance with sequences after the sequence had been read (:issue:`1278`) * Fixed JSON export of numeric values * Fixed handling of sequences of unknown length that switch to implicit encoding, and sequences with VR **UN** (:issue:`1312`) * Do not load external data sources until needed - fixes problems with standard workflow if `setuptools` are not installed (:issue:`1341`) * Fixed empty **PN** elements read from file being :class:`str` rather than :class:`~pydicom.valuerep.PersonName` (:issue:`1338`) * Fixed handling of JPEG (10918-1) images compressed using RGB colourspace rather than YBR with the Pillow pixel data handler (:pr:`878`) * Allow to deepcopy a `~pydicom.dataset.FileDataset` object (:issue:`1147`) * Fixed elements with a VR of **OL**, **OD** and **OV** not being set correctly when an encoded backslash was part of the element value (:issue:`1412`) * Fixed expansion of linear segments with floating point steps in segmented LUTs (:issue:`1415`) * Fixed handling of code extensions with person name component delimiter (:pr:`1449`) * Fixed bug decoding RBG jpg with APP14 marker due to change in Pillow (:pr:`1444`) * Fixed decoding for `FloatPixelData` and `DoubleFloatPixelData` via `pydicom.pixel_data_handlers.numpy_handler` (:issue:`1457`)
2021-09-29revbump for boost-libsadam8-15/+16
2021-09-18biology/biolibc: Update to 0.2.0.11bacon4-10/+10
Regenerate man pages with improved auto-c2man Improved formatting and added missing return value sections
2021-09-03biology/peak-classifier: Update to 0.1.1.21bacon3-9/+9
Fix regression: Replace BL_BED_SET_STRAND() macro with bl_bed_set_strand(), which performs sanity checks
2021-09-03biology/biolibc: Update to 0.2.0.1bacon4-9/+10
Fix regression: Replace BL_BED_SET_STRAND() macro with bl_bed_set_strand(), which performs sanity checks
2021-09-01py-pydicom: PLIST fixadam1-1/+7
2021-08-31biology/Makefile: Add biolibc-toolsbacon1-1/+2
2021-08-31biology/biolibc-tools: import biolibc-tools-0.1.0.36bacon4-0/+37
Biolibc-tools is a collection of simple, fast, and memory-efficient programs for processing biological data. These programs built on biolibc are not complex enough to warrant separate projects.
2021-08-29py-pydicom: add ALTERNATIVESadam1-0/+1
2021-08-29py-pydicom: updated to 2.2.1adam3-197/+313
Version 2.2.0 Changes Data elements with a VR of AT must now be set with values acceptable to Tag(), and are always stored as a BaseTag. Previously, any Python type could be set. BaseTag.__eq__() returns False rather than raising an exception when the operand cannot be converted to BaseTag DA.__str__(), DT.__str__() and TM.__str__() return valid DICOM strings instead of the formatted date and time representations If comparing FileDataset instances, the file metadata is now ignored. This makes it possible to compare a FileDataset object with a Dataset object. rle_encode_frame() is deprecated and will be removed in v3.0, use compress() or RLELosslessEncoder instead. read_file() is deprecated and will be removed in v3.0, use dcmread() instead. write_file() is deprecated and will be removed in v3.0, use dcmwrite() instead. Data dictionaries updated to version 2021b of the DICOM Standard Dataset no longer inherits from dict Enhancements Added a command-line interface for pydicom. Current subcommands are: show: display all or part of a DICOM file codify to produce Python code for writing files or sequence items from scratch. Please see the Command-line Interface Guide for examples and details of all the options for each command. A field containing an invalid number of bytes will result in a warning instead of an exception when convert_wrong_length_to_UN is set to True. Private tags known via the private dictionary will now get the configured VR if read from a dataset instead of UN While reading explicit VR, a switch to implicit VR will be silently attempted if the VR bytes are not valid VR characters, and config option assume_implicit_vr_switch is True (default) New functionality to help with correct formatting of decimal strings (DS) Added is_valid_ds() to check whether a string is valid as a DICOM decimal string and format_number_as_ds() to format a given float or Decimal as a DS while retaining the highest possible level of precision If enforce_valid_values is set to True, all DS objects created will be checked for the validity of their string representations. Added optional auto_format parameter to the init methods of DSfloat and DSdecimal and the DS() factory function to allow explicitly requesting automatic formatting of the string representations of these objects when they are constructed. Added methods to construct PersonName objects from individual components of names (family_name, given_name, etc.). See from_named_components() and from_named_components_veterinary(). Added support for downloading the large test files with the requests package in addition to urllib.request Ensured convert_color_space() uses 32-bit floats for calculation, added per_frame flag to allow frame-by-frame processing and improved the speed by ~20-60% Optimisations for RLE encoding using pydicom (~40% faster). Added support for faster decoding (~4-5x) and encoding (~20x) of RLE Lossless Pixel Data via the pylibjpeg-rle plugin Added Dataset.compress() function for compressing uncompressed pixel data using a given encoding format as specified by a UID. Only RLE Lossless is currently supported Added encoders module and the following encoders: RLELosslessEncoder with ‘pydicom’, ‘pylibjpeg’ and ‘gdcm’ plugins Added read parameter to get_testdata_file() to allow reading and returning the corresponding dataset Handle decoded RLE segments with padding Add option to JSON functions to suppress exception and continue Allow searching FileSet s for a list of elements Added hash function to SR Code Fixes Fixed pickling a Dataset instance with sequences after the sequence had been read Fixed JSON export of numeric values Fixed handling of sequences of unknown length that switch to implicit encoding, and sequences with VR UN Do not load external data sources until needed - fixes problems with standard workflow if setuptools are not installed Fixed empty PN elements read from file being str rather than PersonName Fixed handling of JPEG (10918-1) images compressed using RGB colourspace rather than YBR with the Pillow pixel data handler Allow to deepcopy a ~pydicom.dataset.FileDataset object Fixed elements with a VR of OL, OD and OV not being set correctly when an encoded backslash was part of the element value Fixed expansion of linear segments with floating point steps in segmented LUTs Fixed handling of code extensions with person name component delimiter Fixed bug decoding RBG jpg with APP14 marker due to change in Pillow Fixed decoding for FloatPixelData and DoubleFloatPixelData via pydicom.pixel_data_handlers.numpy_handler Version 2.1.1 Fixes Remove py.typed Fix ImportError with Python 3.6.0 Fix converting Sequences with Bulk Data when loading from JSON Version 2.1.0 Changelog Dropped support for Python 3.5 (only Python 3.6+ supported) Enhancements Large testing data is no longer distributed within the pydicom package with the aim to reduce the package download size. These test files will download on-the-fly whenever either the tests are run, or should the file(s) be requested via the data manager functions. For example: To download all files and get their paths on disk you can run pydicom.data.get_testdata_files(). To download an individual file and get its path on disk you can use pydicom.data.get_testdata_file(), e.g. for RG1_UNCI.dcm use pydicom.data.get_testdata_file("RG1_UNCI.dcm") Added a new pixel data handler based on pylibjpeg which supports all (non-retired) JPEG transfer syntaxes Added apply_rescale() alias Added apply_voi() and apply_windowing() Added prefer_lut keyword parameter to apply_voi_lut() and handle empty VOI LUT module elements Added ability to register external data sources for use with the functions in pydicom.data __contains__, __next__ and __iter__ implementations added to PersonName Added convenience constants for the MPEG transfer syntaxes to pydicom.uid Added support for decoding Waveform Data: Added pydicom.waveforms module and generate_multiplex() and multiplex_array() functions. Added Dataset.waveform_array() which returns an ndarray for the multiplex group at index within a Waveform Sequence element. When JPEG 2000 image data is unsigned and the Pixel Representation is 1 the image data is converted to signed Added keyword property for the new UID keywords in version 2020d of the DICOM Standard Added testing of the variable names used when setting Dataset attributes and INVALID_KEYWORD_BEHAVIOR config option to allow customizing the behavior when a camel case variable name is used that isn’t a known element keyword Added INVALID_KEY_BEHAVIOR config option to allow customizing the behavior when an invalid key is used with the Dataset in operator Implemented full support (loading, accessing, modifying, writing) of DICOM File-sets and their DICOMDIR files via the FileSet class Added AllTransferSyntaxes Added option to turn on pydicom future breaking behavior to allow user code to check itself against the next major version release. Set environment variable “PYDICOM_FUTURE” to “True” or call future_behavior() Added another signature to the bulk_data_uri_handler in from_json to allow for the communication of not just the URI but also the tag and VR to the handler. Previous handlers will work as expected, new signature handlers will get the additional information. pack_bits() can now be used with 2D or 3D input arrays and will pad the packed data to even length by default. Elements with the IS VR accept float strings that are convertible to integers without loss, e.g. “1.0” Added encapsulate_extended() function for use when an Extended Offset Table is required Changes Reading and adding unknown non-private tags now does not raise an exception per default, only when enforce_valid_values is set Data dictionaries updated to version 2020d of the DICOM Standard Updated a handful of the SOP Class variable names in _storage_sopclass_uids to use the new UID keywords. Variables with Multiframe in them become MultiFrame, those with and in them become And, and DICOSQuadrupoleResonanceQRStorage becomes DICOSQuadrupoleResonanceStorage. The following UID constants are deprecated and will be removed in v2.2: JPEGBaseline: use JPEGBaseline8Bit JPEGExtended: use JPEGExtended12Bit JPEGLossless: use JPEGLosslessSV1 JPEGLSLossy: use JPEGLSNearLossless JPEG2000MultiComponentLossless: use JPEG2000MCLossless JPEG2000MultiComponent: use JPEG2000MC In v3.0 the value for JPEGLossless will change from 1.2.840.10008.1.2.4.70 to 1.2.840.10008.1.2.4.57 to match its UID keyword The following lists of UIDs are deprecated and will be removed in v2.2: JPEGLossyCompressedPixelTransferSyntaxes: use JPEGTransferSyntaxes JPEGLSSupportedCompressedPixelTransferSyntaxes: use JPEGLSTransferSyntaxes JPEG2000CompressedPixelTransferSyntaxes: use JPEG2000TransferSyntaxes RLECompressedLosslessSyntaxes: use RLETransferSyntaxes UncompressedPixelTransferSyntaxes: use UncompressedTransferSyntaxes PILSupportedCompressedPixelTransferSyntaxes DicomDir and the dicomdir module are deprecated and will be removed in v3.0. Use FileSet instead pydicom.overlay_data_handlers is deprecated, use pydicom.overlays instead Removed transfer syntax limitations when converting overlays to an ndarray The overlay_data_handlers config option is deprecated, the default handler will always be used. Fixes Dataset.copy() now works as expected Optimistically parse undefined length non-SQ data as if it’s encapsulated pixel data to avoid erroring out on embedded sequence delimiter Fixed get_testdata_file() and get_testdata_files() raising an exception if no network connection is available Fixed GDCM < v2.8.8 not returning the pixel array for datasets not read from a file-like Raise TypeError if dcmread() or dcmwrite() is called with wrong argument Gracefully handle empty Specific Character Set Fixed empty ambiguous VR elements raising an exception Allow apply_voi_lut() to apply VOI lookup to an input float array Fixed Dataset.setdefault() not adding working correctly when the default value is None and not adding private elements when enforce_valid_values is True Version 2.0.0 Changelog Dropped support for Python 2 (only Python 3.5+ supported) Changes to Dataset.file_meta file_meta now shown by default in dataset str or repr output; pydicom.config.show_file_meta can be set False to restore previous behavior new FileMetaDataset class that accepts only group 2 data elements Deprecation warning given unless Dataset.file_meta set with a FileMetaDataset object (in pydicom 3, it will be required) Old PersonName class removed; PersonName3 renamed to PersonName. Classes PersonNameUnicode and PersonName3 are aliased to PersonName but are deprecated and will be removed in version 2.1 dataelem.isMultiValue (previously deprecated) has been removed. Use dataelem.DataElement.VM instead. Enhancements Allow PathLike objects for filename argument in dcmread, dcmwrite and Dataset.save_as Deflate post-file meta information data when writing a dataset with the Deflated Explicit VR Little Endian transfer syntax UID Added config.replace_un_with_known_vr to be able to switch off automatic VR conversion for known tags with VR “UN” Added config.use_DS_numpy and config.use_IS_numpy to have multi-valued data elements with VR of DS or IS return a numpy array Fixes Fixed reading of datasets with an empty Specific Character Set tag Fixed failure to parse dataset with an empty LUT Descriptor or Red/Green/Blue Palette Color LUT Descriptor element. Made Dataset.save_as a wrapper for dcmwrite Removed 1.2.840.10008.1.2.4.70 - JPEG Lossless (Process 14, SV1) from the Pillow pixel data handler as Pillow doesn’t support JPEG Lossless. Fixed error when writing elements with a VR of OF Fixed improper conversion when reading elements with a VR of OF Fixed apply_voi_lut() and apply_modality_lut() not handling (0028,3006) LUT Data with a VR of OW Fixed access to private creator tag in raw datasets Fixed description of newly added known private tag Fixed update of private blocks after deleting private creator Fixed bug in updating pydicom.config.use_DS_Decimal flag in DS_decimal()
2021-08-28biology/peak-classifier: Update to 0.1.1.20bacon3-9/+10
Updates for libxtend and biolibc API changes
2021-08-28biology/vcf2hap: Update to 0.1.3.12bacon3-8/+9
Updates for libxtend and bioloibc API changes
2021-08-28biology/vcf-split: Update to 0.1.2.14bacon3-8/+9
Updates for libxtend and biolibc API changes
2021-08-28biology/ad2vcf: Update to 0.1.3.31bacon3-8/+9
Updates for libxtend and biolibc API changes Clean up and minor bug fixes
2021-08-28biology/biolibc: Update to 0.2.0bacon5-29/+565
Major API overhaul New classes for FASTA and FASTQ Generate accessor and mutator functions for all classes Generate man pages for all functions and macros Export delimiter-separated-value class to libxtend
2021-06-29py-numpy: "Python version >= 3.7 required."nia1-1/+3
2021-06-23Revbump for MySQL default changenia1-2/+2
2021-06-15biology/Makefile: Add peak-classifierbacon1-1/+2
2021-06-15biology/peak-classifier: import peak-classifier-0.1.1bacon4-0/+43
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF Peaks are provided in a BED file sorted by chromosome and position. The GFF must be sorted by chromosome and position, with gene-level features separated by ### tags and each gene organized into subfeatures such as transcripts and exons. This is the default for common data sources.
2021-06-15biology/biolibc: Update to 0.1.3.2bacon4-9/+10
Add LDFLAGS to allow RELRO
2021-06-11biology/vcf-split: Update to 0.1.2bacon3-8/+9
Updates for new biolibc API Upstream change log: https://github.com/auerlab/vcf-split/releases
2021-06-11biology/vcf2hap: Update to 0.1.3bacon3-8/+9
Updates for new biolibc API Upstream change log: https://github.com/auerlab/vcf2hap/releases
2021-06-11biology/ad2vcf: Update to 0.1.3bacon3-8/+9
Updates for new biolibc API Upstream change log: https://github.com/auerlab/ad2vcf/releases
2021-06-11biology/biolibc: Update to 0.1.3bacon4-16/+52
Import sam_buff_t class and VCF functions from ad2vcf Add BED and GFF support Isolate headers under include/biolibc Numerous small enhancements and fixes Upstream change log: https://github.com/auerlab/biolibc/releases
2021-06-11biology/ncbi-blast+: Update to 2.11.0bacon8-54/+171
Release notes: https://www.ncbi.nlm.nih.gov/books/NBK131777/
2021-06-01*: recursive PKGREVISION bump for sneaky gsl shared library version number ↵wiz1-3/+2
change
2021-05-29biology/minimap2: install minimap2 program instead of python bindingbrook2-19/+11
The distfile for minimap2 includes two different components: (i) the minimap2 sequence mapping program itself, and (ii) a python binding generally referred to as mappy. The initial version of this package included only the python binding. However, it is more appropriate that the minimap2 package should contain the program of the same name, and a new package be created with the name mappy for the python binding. Splitting these into two packages makes sense, because this allows users to install the minimap2 package without python dependencies.
2021-05-27biology/filter-fastq: add filter-fastq version 0.0.0.20210527brook1-1/+2
2021-05-27biology/filter-fastq: add filter-fastq version 0.0.0.20210527brook4-0/+56
Filter reads from a FASTQ file using a list of identifiers. Each entry in the input FASTQ file (or files) is checked against all entries in the identifier list. Matches are included by default, or excluded if the --invert flag is supplied. Paired-end files are kept consistent (in order). This is almost certainly not the most efficient way to implement this filtering procedure. I tested a few different strategies and this one seemed the fastest. Current timing with 16 processes is about 10 minutes per 1M paired reads with gzip'd input and output, depending on the length of the identifier list to filter by. usage: filter_fastq.py [-h] [-i INPUT] [-1 READ1] [-2 READ2] [-p NUM_THREADS] [-o OUTPUT] [-f FILTER_FILE] [-v] [--gzip]
2021-05-26Added biology/beagle version 5.2brook1-1/+2
2021-05-26biology/beagle: added beagle 5.2brook7-0/+143
Introduction Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Beagle version 5.2 provides significantly faster genotype phasing than version 5.1 Citation If you use Beagle in a published analysis, please report the program version and cite the appropriate article. The Beagle 5.2 genotype imputation method is described in: B L Browning, Y Zhou, and S R Browning (2018). A one-penny imputed genome from next generation reference panels. Am J Hum Genet 103(3):338-348. doi:10.1016/j.ajhg.2018.07.015 The most recent reference for Beagle's phasing method is: S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097. doi:10.1086/521987 This reference will be updated when the Beagle version 5 phasing method is published.
2021-05-26Added biology/racon 1.4.3brook1-1/+2
2021-05-26biology/racon: add racon 1.4.3brook4-0/+53
## Description Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Racon can be used as a polishing tool after the assembly with **either Illumina data or data produced by third generation of sequencing**. The type of data inputed is automatically detected. Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files **can be compressed with gzip** (which will have impact on parsing time). Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads **including dual overlaps**. A **wrapper script** is also available to enable easier usage to the end-user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be **subsampled** to decrease the total execution time (accuracy might be lower) while target sequences can be **split** into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well.
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-15 21:35:53 +0000