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CHANGELOG
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# 0.2.12 (02.08.18)
- Fix bug in bigwig creation (due to new pd behavior)
# 0.2.11 (01.08.18)
- Massive speedup with Cython
- Fix bugs added by 0.2.10
# 0.2.10 (31.07.18)
- Use categoricals for memory efficiency and speed
- Fix bug in epic when using chromsizes
# 0.2.9 (12.02.18)
- add pseudocounts in sum log2fc bigwigs to avoid inf
- epic-merge: do not remove bins without any counts if they are enriched
- fix outputting of debugging info ("chr1_before_find_islands.csv")
# 0.2.8 (16.01.18)
- various updates to epic-cluster
- epic-cluster now can create bigwig
- add C. Elegans genomes (ce10, ce11)
- add pseudocounts to ChIP to avoid -inf in bigwigs
# 0.2.7 (12.12.17)
- Add bed with region statistics to epic-cluster output
- Fix bug due to new concat of empty dfs behavior in Pandas
- Fix bug that split enriched regions that should have been whole.
- Fix for new NA behavior
- Fix epic-merge with regions
# 0.2.6 (13.11.17)
- fix issue #66 (thanks nw11)
# 0.2.5 (22.08.17)
- add epic-count script
- add epic-blacklist script
- fix bug in paired end mode (thanks to Assa Yeroslaviz for reporting)
- about 80 new UCSC genomes added!
# 0.2.4 (28.07.17)
- add pseudocount to input when computing `--individual-log2fc-bigwigs`
# 0.2.3 (25.07.17)
- fix RPKM normalization in bigwigs
- add `--individual-log2fc-bigwigs` flag, which creates a log2fc bigwig of the ChIP divided by all the normalized input.
# 0.2.2 (21.07.17)
- Change flag --effective_genome_fraction to --effective-genome-fraction
- Fix autoinferring of bed/bedpe when files are (b/g)zipped
- Use log2FC in output, not raw fold change
- Now separate flags for sum bigwigs: --chip-bigwig and --input-bigwig
- Add support for log2FC bigwig: --log2fc-bigwig
# 0.2.1 (20.07.17)
- Fix bug
# 0.2.0 (19.07.17)
- Fix teensy 2.7 bug
# 0.1.29 (19.07.17)
- Add log flag
- Add outfile flag
- Write results before creating bigwigs/matrix in case the latter fails
# 0.1.28 (19.07.17) BREAKING CHANGES
- now autoinfers paired end so can mix pe and non-pe files
- effective_genome_size renamed effective_genome_fraction
# 0.1.27 (18.07.17)
- epic-cluster script to cluster islands across experiments
- ensure files given on command line exist
- fix bug in matrix concat due to no enriched regions in some chromosomes
# 0.1.26 (28.06.2017)
- squash another multiproc bug
# 0.1.25 (20.01.2017)
- work around pandas multiprocessing bug in matrix/bigwig creation
# 0.1.24 (11.01.2017)
- change the default FDR cutoff from 1 to 0.05
- -k/--keep-duplicates argument is now a proper flag
# 0.1.23 (15.11.2016)
- (internal): add mypy/PEP484 typing to code. Thanks Ryan C. Thompson.
- fix bug where shuffling of columns happen in epic-merge
- fix error when no tmpdir was set in epic-effective
# 0.1.22 (09.11.2016)
- add epic-merge script to merge matrixes from multiple experiments into one
- fix bugs and bad logic in epic-overlaps script
- allow renaming axes and legend in epic-overlaps
# 0.1.21 (18.10.2016)
- add argument --chromsizes/-cs to allow for custom genomes, assemblies and simulated data
- use pyBigWig to create bigwigs, drop R/bioconductor dependencies
- argument effective_genome_length renamed to effective_genome_size
- epic-overlaps script to graph overlapping regions/nucleotides for differential ChIP-Seq (experimental)
# 0.1.20 (04.10.2016)
- create bed file with -b option (for genome browsers or downstream analysis)
- create sum bigwigs with -sbw option
# 0.1.19 (03.10.2016)
- print pandas and epic version on startup
- remove all bedgraph options
- remove summary bigwig options
- now only creates individual bigwigs
# 0.1.18 (06.09.16)
- add hg18
# 0.1.17 (30.08.16)
- fix rare bug in bigwig creation
# 0.1.16 (30.08.16)
- remove out of bounds bins before creating bedgraph
# 0.1.15 (26.08.16)
- add options --bigwig/-bw and --individual-bigwig/-ibw to store bigwig files
# 0.1.14 (24.08.16)
- add options --bedgraph/-b and --individual-bedgraph/-ib to store bedgraph files
# 0.1.13 (15.08.16)
- add susScr2 genome
# 0.1.12 (15.08.16)
- work around Pandas "source array is read only bug"
- now accepts genome names in any case
- if genome not found, list available genomes
# 0.1.11 (12.08.16)
- add susScr3
# 0.1.10 (12.08.16)
- add rn4, rn5, rn6
# 0.1.9 (11.08.16)
- fix another importerror
# 0.1.8 (11.08.16)
- fix importerror in edge case
- allow bed files to have different number of chromosomes
# 0.1.7 (11.08.16)
- remove bug when finding window counts for paired end
# 0.1.6 (10.08.16)
- enable --store-matrix option for paired end data
- fix error in merging chip and input for paired end data
- fix error message in merge chip and input
# 0.1.5 (09.08.16)
- add better error message in the function to merge chip and input
# 0.1.4 (09.08.16)
- fix bugfix: now zipped pe files properly handled (thanks to Piotr Balwierz for re-reporting)
# 0.1.3 (08.08.16)
- added new setup file for bioconda install
# 0.1.2 (08.08.16)
- bugfix: fixed lacking zip handling for paired end files (thanks to Piotr Balwierz for reporting)
# 0.1.1 (06.07.16)
- bugfix: effective genome size was way off for hg38
- add danRer7 and danRer10 genomes
# 0.1.1 (06.07.16)
- bugfix: effective genome size was way off for hg38
- add danRer7 and danRer10 genomes
# 0.1.0 (20.06.16)
- speed up writing matrix to file
# 0.0.10 (11.06.16)
- remove support for .bam files, use bed/bedpe instead
# 0.0.9 (10.06.16)
- store matrixes of counts per bin for chip and input with flag --store-matrix <outfile_prefix> (these files can be massive, might be slow)
- use median readlength to find effective genome size, not mean
# 0.0.8 (24.05.16)
- add snakemake-workflow to get all genome data (thanks Ryan Dale)
- new flag: effective genome length
- epic now automatically finds the correct effective genome size
- effective genome sizes updated, will lead to slightly different results
- internal: add chromsizes to package and use pkg_utils to get them
- fix bug: used bedToBam when meant to call bamToBed
# 0.0.7 (06.05.16)
- fix default value of keep duplicates (was True, now is False)
- fix max-gap bug (max gap used was actually max-gap - 1)
- (internal: no more functions with > 5 arguments)
- (the difference between SICER and epic I thought was a due to a bug, was caused
by them having different genome versions as default)
# 0.0.6 (10.04.16)
- add script to compute the effective genome size (thanks to Heng Li for alerting me to the existence of jellyfish2)
# 0.0.5 (07.04.16)
- remove Pandas only option. Now unix is required.
- change to argparse instead of docopt (thanks Dario Beraldi)
- separate args for control and input files (thanks Dario Beraldi)
- print cl-args exactly as recieved (thanks to Istvan Albert for pointing out glitch)
- add version info
- add support for bam files (requires bedtools)
- fix "bug" that prints chromosome start and end in output as floats.
- change output format to use tab as delimiter and underscore as within name delimiter ("P_value", not "P value")