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CHANGELOG.txt
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v2.0.4 (2023-09-08)
- Fix issue with wrong behavior of fragment building and usage during gene quantification and coverage
v2.0.3 (2022-09-30)
- Fix zenodo web hook
v2.0.2 (2022-09-30)
- Change License from ISC License to MIT License
v2.0.1 (2022-08-23)
- Accelerate fragment building for paired-end reads
- Set color blind friendly colors for viz align plots
v2.0.0 (2022-06-28)
- Added multi-species analysis (changes the API)
- Results of subcommands separated by species
- Updated mapping statistics (e.g. count species-cross aligned reads)
- Include or exclude species-cross aligned reads in read counts and/or normalization
- Additional vizualisation for multi-species projects
- Template fragment building for paired-end reads
- Subcommands (for paired-end reads) use counts and/or normalization based on fragments or single reads
- Filter reads by template length
- Output folder creation only when calling the corresponding subcommands
v1.0.5 (2021-10-12)
- Fixed a bug of package creation, where the old build was not removed prior to cration
v1.0.4 (2021-10-12)
- Set biopython install requirements to v1.78
- Bugfix wheel package
v1.0.3 (2021-10-08)
- Bugfix in gff3 parser
v1.0.2 (2021-10-08)
- Fixed segemehl tests
- Gene quantification: Removed normalization by number of splits
- Hotfix of calculating TMPs with zero values
v1.0.1 (2020-07-11)
- Hotfix of align error caused by realign arg still present
v1.0.0 (2020-07-08)
- Added calculation of TPM (transcripts per million)
- Added automated integration of subcommands and parameters to the documentation
v0.6.0 (2020-05-22)
- changed behaviour of gene quantification regarding sense and anti-sense
--add-antisense instead of --skip-antisense and added --antisense-only
- avoid writing of unmapped reads to final bam
- moved documentation to https://reademption.readthedocs.io
- integration of TravisCI
v0.5.0 (2019-07-15)
- Addapted to segemehl 0.3.4
- Several clean-ups
v0.4.5 (2017-12-31)
- Move documentation to Read the Docs
- New theme for docs
v0.4.4 (2017-12-31)
- Fix issue with unnecessary gene quanti
- Fix issue of DESeq2 MA plot generation
v0.4.3 (2016-09-06)
- Fix problem with current version of DESeq2
v0.4.2 (2016-08-29)
- Replace ugly pysam view construct (thanks to Thorsten Bischler)
v0.4.1 (2016-08-02)
- Fix another issue with pysam in samtobam.py
- Update dependencies
v0.4.0 (2016-07-27)
- Fix issue with pysam in samtobam.py
- Update installation documentation
v0.3.9 (2016-03-07)
- Add support for centered approach in coverage and gene_quanti
(by Thorsten Bischler)
- Fix bar chart creation in viz_gene_quanti (by Thorsten Bischler)
- Fix style for matplotlib
- Fix MA plots
v0.3.8 (2016-03-03)
- Add last base coverage option (by Thorsten Bischler)
- Numerous fixes (several from Thorsten Bischler)
- Change to bdist_wheel (PEP 0427)
v0.3.7 (2015-07-03)
- Add --reverse_complement flag to align subcommand
- Use lib name instead of condition for DESeq2 heatmap
- Add error explanation when GTF/GFF2 annotation files are used
v0.3.6 (2015-03-18)
- Add strand-unspecific read per gene quantification
v0.3.5 (2015-01-13)
- Update some pysam related function due to changes in API changes of pysam
- Add further requirements (matplotlib, Biopython, pandas)
- Reimplement MA plot generation
- Add strand-unspecific coverage calculation
- Several small code improvements
v0.3.4 (2014-08-23)
- Fix bug with paired-end suffix
- Fix bug with paired-end mapping stats table
- Add Docker documentation
- Update reference
v0.3.3 (2014-07-20)
- Fix bug in mapping stats table generation
- Add further mapping success value (use reads that are long enogh
after read processing as reference)
- Improve Makefile
v0.3.2 (2014-07-12)
- Add quality trimming and adapter clipping (for reviewer Matt
MacManes)
- Update documentation
v0.3.1 (2014-07-05)
- Add live / installation image (for anonymous reviewer #1)
- Add support for Fastq read files (for anonymous reviewer #3)
- Extend CLI documentation (for reviewer Matt MacManes)
- Fix/extend online documentation (thanks for help re. OS X to Lei Li
and the feedback to Petya Zhelyazkova)
v0.3.0 (2014-05-18)
- Improve Makefile
- Update docs
- Add read mapping stats
v0.2.9 (2014-05-12)
- Remove redundant read mapping stat calling
- Bug fix for crossmapped read removal
v0.2.8 (2014-05-09)
- Add removal of crossmapped reads
- Fix bug in align subcommand (reported by Alexander Mellmann)
- Adapt description of the DESeq2 installation
v0.2.7 (2014-05-03)
- Update docs
- Improve Makefile
- Fix bug - no align stat creation if realigning was not acitivated
v0.2.6 (2014-04-10)
- Fix error with newer R
- Add error/solution for older DESeq2 version
v0.2.5 (2014-04-05)
- Add troubleshooting page to docs
v0.2.4 (2014-04-05)
- Add logo
v0.2.3 (2014-04-01)
- Improve documentation
- Modify README
- Extend Makefile
v0.2.2 (2014-03-31)
- Fix setup.py
- Typos fixing
v0.2.1 (2014-03-31)
- Improve documentation
- Add badges and further info to Readme
- Extend Makefile
v0.2.0 (2014-03-29)
- Switch to DESeq
- Renaming from TRAPL to READemption (yes, another name change)
v0.1.9 (2014-02-17)
- Fix isssue with path for paired-end reads
- Fix lib name sorting for gene quanti overview
- Improve README file
v0.1.8 (2014-01-16)
- Add realigning of unmapped reads
- Change of CLI parameters
- And additionaly parameter for coverage normalisation
v0.1.7 (2014-01-09)
- Package generation for distribution
- Name change from RAPL to TRAPL due to name clash with other tool
- Add support for paired end reads
- Documentation extention and futher comments
- Several fixes and minor changes
- Cleaning
- Add a Makefile for import dev tasks
v0.1.6 (2013-09-16)
- Change coverage normalization for the case that only uniquely aligned
reads are taken into account
v0.1.5 (2013-08-16)
- Add serveral visualizations methods
- Misc small changes
v0.1.4.1 (2013-07-08)
- Fix issue with lib names in deseq
v0.1.4 (2013-06-28)
- Change output folder structure
- Add parallel processing of gene quantification
- Add output file existance test for the gene quantification
- Add consideration for split alignment in gene quantification
- Add removal of common file suffixes for lib names
- Store R session info
- Suppress segemehl output
- Several minor improvements
v0.1.3 (2013-06-17)
- Add output file existance test for the alignment step
v0.1.2 (2013-06-13)
- Add read splitting
v0.1.1 (2013-05-25)
- Add parameter for polyA-clipping
v0.1 (2013-04-25)
- Very first official version