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iqbal-lab-org
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gramtools
Genome inference from a population reference graph
MIT License
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Release 0.5 requirements
#72
iqbal-lab
closed
6 years ago
5
Faster kmer hashing
#71
ffranr
opened
6 years ago
14
Beginning of read matching within allele site and crossing into a non-variant region
#70
ffranr
closed
6 years ago
5
bug in tip of all_optimizations_stable branch
#69
sm0179
closed
6 years ago
0
assertion crash for certain reads in version with merged optimisations
#68
sm0179
closed
6 years ago
1
FM-Index construction avoided if cached version found
#67
ffranr
closed
6 years ago
1
Quasimap reads concurrently
#66
ffranr
closed
6 years ago
1
Write tests for mapping functionality (map.cpp)
#65
ffranr
closed
6 years ago
1
Rename "precalc" to "kmers_index"
#64
ffranr
closed
6 years ago
1
Improve tests in test_bidir_search.cpp
#63
ffranr
closed
6 years ago
1
Remove pthread code from kmers indexing routine
#62
ffranr
closed
6 years ago
0
Ensure SDSL runtime tempoary files are unique to each gramtools instance
#61
ffranr
closed
6 years ago
1
Performance of kmers generation routine too dependant on variant site distribution
#60
ffranr
closed
6 years ago
2
Remove tempoary files side effects form tests
#59
ffranr
closed
6 years ago
1
Write tests for precalc file generation code
#58
ffranr
closed
6 years ago
1
Steps for generating SA intervals for kmers
#57
ffranr
closed
6 years ago
2
Separate functionality: masks generation from kmers generation
#56
ffranr
closed
6 years ago
1
variantKmers script is not pulling out all the right kmers
#55
iqbal-lab
closed
6 years ago
7
variantkmers script error
#54
sm0179
closed
7 years ago
7
Add --min-allele-freq argument to build command
#53
sm0179
opened
7 years ago
4
Ensure build finished succesfully before executing quasimap
#52
ffranr
closed
6 years ago
1
Change --reference argument to --fastaq
#51
ffranr
closed
7 years ago
2
Excesive memory consumption whilst precalculating kmers
#50
ffranr
closed
6 years ago
1
Kmer generation fails silently when Biopython module not installed for python2.7
#49
ffranr
closed
7 years ago
1
gramtools no longer compiles on refactor_bidir_bwd
#48
iqbal-lab
closed
7 years ago
5
Faster/lower RAM kmer hash
#47
iqbal-lab
closed
6 years ago
1
Add size equal asserts for: linear PRG, site mask, and allele mask
#46
sm0179
closed
6 years ago
3
Add tests to linear PRG construction script
#45
sm0179
closed
6 years ago
3
k-mers overlapping variants
#44
sm0179
closed
6 years ago
1
Move fm-index construction to build step
#43
sm0179
closed
6 years ago
1
Store bitmask over BWT to file during build step
#42
sm0179
closed
6 years ago
1
Store ranks over BWT to file during build step
#41
sm0179
closed
6 years ago
1
Move kmers indexing to build step
#40
sm0179
closed
6 years ago
1
coverages obtained with bitmask branch on joint DBLMSP prg
#39
sm0179
closed
6 years ago
2
Typo - festa
#38
iqbal-lab
closed
7 years ago
2
Minor updates on install notes, and refactored Makefile.
#37
jeromekelleher
closed
7 years ago
1
Add toy data to allow new user try out the code
#36
jeromekelleher
closed
6 years ago
4
Unexpected assertion for specific kmer
#35
iqbal-lab
closed
7 years ago
3
Segfault in latest unit test of multiple matches
#34
iqbal-lab
closed
7 years ago
5
bidir_search_fwd is broken
#33
iqbal-lab
closed
6 years ago
6
Something odd with sites object in unit test for forward bidir search
#32
iqbal-lab
closed
6 years ago
4
100a/36a test is too slow
#31
iqbal-lab
closed
7 years ago
10
TwoSNPs unit tests shows sites object storing same site-id for both SNPs
#30
iqbal-lab
closed
7 years ago
1
Periodic assertion failures in SDSL
#29
iqbal-lab
closed
6 years ago
1
Valgrind finds Invalid read (means bad memory access) in BackwardSearchTest.NoVariants1
#28
iqbal-lab
closed
7 years ago
5
Fails to map/match to a PRG with no variation
#27
iqbal-lab
closed
7 years ago
1
Pointing gramtools at current SDSL results in assertion failure in unit tests
#26
iqbal-lab
closed
6 years ago
7
Read mapping fails due to bidir_search returning an interval [a,a)
#25
iqbal-lab
closed
8 years ago
1
False interval added in precalc
#24
iqbal-lab
closed
6 years ago
0
Underflowing a uint64_t leads to unexpected lack of problems
#23
iqbal-lab
closed
8 years ago
2
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