tskit-dev/tskit: C API 1.0.0
Authors/Creators
- Jerome Kelleher1
- Ben Jeffery2
- Yan Wong
- Peter Ralph3
- Georgia Tsambos4
- Daniel Goldstein5
- Kevin R. Thornton6
- Anthony Wilder Wohns7
- pyup.io bot8
- Hugo van Kemenade9
- Brian Zhang
- Murillo R.3
- Castedo Ellerman10
- Graham Gower11
- Clemens Weiss
- Jeremy Guez
- Savita Karthikeyan
- Inés Rebollo
- Saurabh Belsare12
- Andrew Kern3
- marianne-aspbury
- Jeet Sukumaran13
- Jonathan Terhorst
- Roohy (Ruhollah) Shemirani14
- Shing Hei Zhan15
- Ivan Krukov
- Nik Baya
- 1. Big Data Institute
- 2. Oxford University
- 3. University of Oregon
- 4. University of Melbourne
- 5. Broad Institute of MIT and Harvard
- 6. University of California Irvine
- 7. Broad Institute
- 8. @pyupio
- 9. Nord Software
- 10. geneheritage.com
- 11. University of Copenhagen
- 12. Kern-Ralph Co-Lab, University of Oregon
- 13. http://sukumaranlab.org
- 14. Icahn School of Medicine at Mount Sinai
- 15. University of Oxford
Description
This major release marks the point at which the documented API becomes stable and supported.
Breaking changes
Change the type of genotypes to
int32_t, removing theTSK_16_BIT_GENOTYPESflag option. (@benjeffery, #463, #2108)tsk_variant_tnow includes itstsk_site_trather than pointing to it. (@benjeffery, #2161, #2162)Rename
TSK_TAKE_TABLEStoTSK_TAKE_OWNERSHIP. (@benjeffery, #2221, #2222)TSK_DEBUG,TSK_NO_INIT,TSK_NO_CHECK_INTEGRITYandTSK_TAKE_OWNERSHIPhave moved tocore.h(@benjeffery, #2218, #2230))Rename several flags:
- All flags to
simplifyfor exampleTSK_KEEP_INPUT_ROOTSbecomesTSK_SIMPLIFY_KEEP_INPUT_ROOTS. - All flags to
subsetfor exampleTSK_KEEP_UNREFERENCEDbecomesTSK_SUBSET_KEEP_UNREFERENCED. TSK_BUILD_INDEXES->TSK_TS_INIT_BUILD_INDEXESTSK_NO_METADATA->TSK_TABLE_NO_METADATATSK_NO_EDGE_METADATA->TSK_TC_NO_EDGE_METADATA
(@benjeffery, #1720, #2226, #2229, #2224)
- All flags to
Remove the generic
TSK_ERR_OUT_OF_BOUNDS- replacing with specific errors. RemoveTSK_ERR_NON_SINGLE_CHAR_MUTATIONwhich was unused. (@benjeffery, #2260)Reorder stats API methods to place
resultas the last argument. (@benjeffery, #2292, #2285)
Features
Make dumping of tables and tree sequences to disk a zero-copy operation. (@benjeffery, #2111, #2124)
Add
edgeattribute tomutation_tstruct and make available in tree sequence. (@jeromekelleher, #685, #2279)Reduce peak memory usage in
tsk_treeseq_simplify. (@jeromekelleher, #2287, #2288)
Files
tskit-dev/tskit-C_1.0.0.zip
Files
(1.1 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/tskit-dev/tskit/tree/C_1.0.0 (URL)