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CHANGELOG.md

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v0.20.1

  • Remove use of deprecated max_chunk argument from cooler tile fetcher.

v0.20.0

  • remove numpy from setup requires
  • Use builtin warnings module instead of relying on alias from numpy.
  • Replace instances of .iteritems() with .items()

v0.19.0

  • Fix decoding error in multivec tileset info
  • Allow JSON in multivec tileset info

v0.18.1

  • Don't pin versions in requirements.txt

v0.18.0

  • Added bigwigs_to_multivec command
  • Bumped dask version
  • Bumped pandas version

v0.17.1

  • Fix narrow npmatrix tile fetching bug

v0.17.0

  • Updated the BAM file fetcher to do more efficient substitution loading
  • Include strand, cigars, and other metadata from reads
  • Added tabix loader that can be estimated to estimate the size of data in a region of a BAM file
  • Add FASTA tileset

v0.16.0

  • Return chromsizes as a single array in beddb tileset_info
  • [BREAKING] Remove the chrom_names and chrom_sizes fields in the beddb tileset info

v0.15.4

  • Remove type=bool from bedpe aggregate function to fix "Got secondary option for non-boolean flag" error
  • No default assembly

v0.15.2

  • More informative error message when doing bedfile_to_multivec conversion

v0.15.1

  • Added support for multivec row_infos stored under /info/row_infos as an hdf5 utf-8 string dataset.

v0.15.0

  • Improve performance of clodius aggregate bedpe using sqlite batch inserts, transactions, and PRAGMAs
  • Show default values for clodius aggregate bedpe -h
  • Add short options to clodius aggregate bedpe
  • Make clodius aggregate bedpe --chromosome actually do something
  • For bedpedb 1D tiles, retrieve entries where either regions at least partially overlaps with a tile
  • Harmonize bedpedb tile getter names

v0.14.3

  • Small bug when retrieving tile 0.0 from bam files
  • More accurate generation of multivec tiles that span across chromosomes

v0.14.2

  • Make sure that chromsizes are serialized as ints

v0.14.1

  • Natural ordering of bam file chromosomes

v0.14.0

  • Add "name" field to beddb format

v0.13.1

  • Fix returned header values

v0.13.0

  • Ran black on the entire code base
  • Introduced versions to beddb and bed2ddb files
  • Added zoom level to the r-tree index

v0.12.0

  • Added tile queries for bigBed files, using score data (if available) to threshold those elements returned, based on a specified or default maximum.

v0.11.5

  • Add tiles function and test for multivec. It can be used in higlass-python and higlass server.

v0.11.4

  • Modified bedfile_to_multivec conversion to retain lines in which the end coordinate is not a multiple of the resolution. It adds an extra bin for the remainder. It also displays an error when start coordinate is not multiple of resolution
  • Fix bug to handle headers.
  • Modified create_multivec_multires for states files to show only the contents of the first column of the row_infos file as the name of the state.

v0.11.3

  • Maintenance: Switched from nose to pytest and added coverage reporting.
  • Use columnar format for BAM reads return values

v0.11.2

  • Added max_tile_width parameter to ct.bam.tiles() so that users can set a limit on how large of a region data is returned for

v0.11.0

  • Added bamfile support

v0.10.12

  • Simplified density tiles generator.
  • Fix error with npvector tileset_info.
  • Add __version__.

v0.10.11

  • Calculate np.nan on the fly if not available for npvector tracks

v0.10.10

  • Fix error in bedfile_to_multivec conversion when encountering value-less files
  • Update the bedpe aggregator to fix the error in using a chromsizes file
  • Make tsv_to_mrmatrix more flexible and add it to the exported scripts.
  • Display more meaningful error messages when encountering unknown chromosomes or assemblies
  • Removed redundant multivec function
  • Removed obsolete bigwig function
  • Make tsv_to_mrmatrix more flexible and add it to the exported
  • Detect non-symmetric square coolers using the storage-mode metadata. Support for the symmetric property is retained for the legacy mcool format.

v0.10.7

  • Changed bins_per_dimension in npvector.tileset_info to match the value in in npvector.tiles (1024)

v0.10.5

  • Removed slugid decode

v0.10.2 (2019-02-06)

  • new option to import a "states" file format, a bed file with categorical data, e.g. from chromHMM to multivec format.
  • while converting a bed file to multivec, each segment can now be a multiple of base_resolution, rather than exactly match the base_resolution

v0.10.1 (2019-01-22)

  • Removed a buggy print statement from the conversion script

v0.9.5 (2018-11-11)

  • If the start position is greater than the end position, switch them around

v0.9.0 (2018-05-07)

  • Removed clodius aggregate bigwig

v0.8.0 (2018-05-06)

  • Bug fixes
  • GeoJSON aggregation
  • Multivec tiles

v0.7.4 (2018-02-14)

  • Greatly sped up bedfile aggregation and fixed the maximum per tile limiting

v0.7.3 (2018-01-31)

  • Use random importance by default

v0.7.2 (2017-12-04)

  • Populate the xEnd field

v0.7.1 (2017-12-04)

  • Added the 'header' field to beddb tiles

v0.7.0 (2017-10-04)

  • Replaced get_2d_tile with get_2d_tiles
  • Replaced get_tile with get_tiles

v0.6.5 (2017-07-14)

  • Added a delimiter option to bedfiles
  • Fixed beddb uid decoding
  • Adding decoding to slugid.nice() methods

v0.6.0-0.6.4 (2017-07-13)

  • python3 support

v0.5.0

  • Added clodius aggregate bedpe
  • More extensive unit tests

v0.4.7

  • Renamed tsv to bedlike

v0.4.6

  • Bug fixes in tile-text-file (tsv tiling)

v0.4.3

  • When extracting a certain chromosome, place features at the position of the chromosome