Recent Releases of https://github.com/cancerit/cgpbigwig
https://github.com/cancerit/cgpbigwig - 1.5.2 - Add bg2bw checks for sorting
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Published by davidrajones over 5 years ago
https://github.com/cancerit/cgpbigwig - 1.5.1 - libdeflate
htslib and related tools now compiled with libdeflate for performance improvements.
No impact on result.
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Published by keiranmraine over 5 years ago
https://github.com/cancerit/cgpbigwig - 1.5.0 - maintenance release
Updates libraries:
- htslib to 1.11
- libBigWig to 0.4.4
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Published by keiranmraine over 5 years ago
https://github.com/cancerit/cgpbigwig - 1.4.0 - Import cwls and examples to core cgpBigWig repo
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Published by davidrajones over 5 years ago
https://github.com/cancerit/cgpbigwig - 1.3.0 - maintenance release
No changes to in/output:
- Update to htslib 1.10.2
- Update base image to Ubuntu 20.04
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Published by keiranmraine over 5 years ago
https://github.com/cancerit/cgpbigwig - Add bam2bw -S/--scale-log10 to enable simple RPKM rescaling.
1.2.0
Add bam2bw -S/--scale-log10 to enable simple RPKM rescaling. Thanks to @shouldsee for these modifications.
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Published by davidrajones almost 6 years ago
https://github.com/cancerit/cgpbigwig - 1.1.0 - Docker within primary repo
Docker build now directly linked to code. This change is made to allow large scale real data CI testing.
dockstore-cgpbigwig will be modified to only contain CWL and will essentially just retag this image.
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Published by keiranmraine over 6 years ago
https://github.com/cancerit/cgpbigwig - 1.0.2 - Hotfix GRCh38 contig parsing
1.0.2
- Correct region parsing in bam2bw to cope with GRCh38 contigs
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Published by almost 8 years ago
https://github.com/cancerit/cgpbigwig - 1.0.1 - Hotfix to bam2bw
- Fix bam2bw. Single region string and -z caused header issues.
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Published by almost 8 years ago
https://github.com/cancerit/cgpbigwig - 1.0.0 - Overlapping read support added
1.0.0
- First full release
- Add overlapping reads support to
bam2bw,bam2bwbasesandbam2bedgraphvia commandline flag--overlap-a- If the same readname is encountered twice at a position it is considred an overlapping read pair.
- Where the same base [ACGT] was encountered on each of the reads it will only be counted once. If a different base was encountered then the coverage count is incremented once for each base.
- Updated License headers with new email address
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Published by almost 8 years ago
https://github.com/cancerit/cgpbigwig - 0.5.0 - HTSLib / libbigwig update
- Update to HTSlib 1.7 (for consistency across tools)
- Update to libBigWig 0.4.2
- Some README.md and INSTALL.md updates
- Thanks go to jsmedmar for documentation contributions
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Published by about 8 years ago
https://github.com/cancerit/cgpbigwig - Hotfix - 0.4.4 bam2bw fix for incorrect contig
- Correct parseRegionString return type. Fixes #11.
- Above change also fixes #12.
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Published by over 8 years ago
https://github.com/cancerit/cgpbigwig - Hotfix - 0.4.3 - LibBigWig update
Fixes #10 Updated libBigWig to version 0.3.4
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Published by over 8 years ago
https://github.com/cancerit/cgpbigwig - Hotfix - 0.4.2 - Permits GRCh38 contig name parsing
- Modified parsing of regions to enable names with : in (i.e. GRCh38)
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Published by almost 9 years ago
https://github.com/cancerit/cgpbigwig - 0.4.1
- Updated libBigWig to 0.3.1 - fixes issue with overflow in very large zoom levels
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Published by about 9 years ago
https://github.com/cancerit/cgpbigwig - 0.4.0
- Added detectExtremeDepth code. Replaces functionality in PCAP-core detectExtremeDepth.pl
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Published by about 9 years ago
https://github.com/cancerit/cgpbigwig - 0.3.1
- Changes HTSlib to 1.3.2 (bringing all stack in line)
- Changed libBigWig archive get to use release rather than commit id (actually the same but harder to tell which release it is)
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Published by keiranmraine about 9 years ago
https://github.com/cancerit/cgpbigwig - 0.3.0
- Changes to setup.sh to permit OSX installation
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Published by over 9 years ago
https://github.com/cancerit/cgpbigwig - Bugfix release - 0.2.1
Fixes #4 Changes to logic to cope with ends of regions and zero regions.
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Published by over 9 years ago
https://github.com/cancerit/cgpbigwig - 0.2.0
0.2.0
- Added bedgraph to bw functionality via bg2bw
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Published by over 9 years ago