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joshuak94
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BAMIntervalTree
BSD 3-Clause "New" or "Revised" License
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[MISC] update seqan3
#44
Irallia
closed
2 years ago
0
Fix bugs related to read lengths.
#43
joshuak94
closed
2 years ago
3
[MISC] Update doxygen & submodule seqan3
#42
Irallia
closed
2 years ago
0
Change default # threads to 1, change benchmarking to use 2 threads, …
#41
joshuak94
closed
2 years ago
0
Update bamit to return vector of records.
#40
joshuak94
closed
2 years ago
1
[FEATURE] Add functionality to sample a bam file for read depth.
#39
joshuak94
closed
2 years ago
1
[MISC] remove warnings from pedantic
#38
Irallia
closed
2 years ago
0
Remove pedantic
#37
joshuak94
closed
2 years ago
0
update seqan.
#36
joshuak94
closed
2 years ago
0
Update seqan
#35
joshuak94
closed
2 years ago
0
Change from specialized input/output types to the default seqan ones.…
#34
joshuak94
closed
2 years ago
0
Add thread option to indexing and overlap queries for BAM decompression.
#33
joshuak94
closed
3 years ago
0
Add const where relevant, change offset variable names to position.
#32
joshuak94
closed
3 years ago
0
Seqan update
#31
joshuak94
closed
3 years ago
0
Add verbose options.
#30
joshuak94
closed
3 years ago
0
Change get_overlap_records to return file offset of first read.
#29
joshuak94
closed
3 years ago
0
Add benchmarking against htslib.
#28
joshuak94
closed
3 years ago
0
Fix trailing empty chromosomes by initializing intervalnode vector to…
#27
joshuak94
closed
3 years ago
0
Update readme
#26
joshuak94
opened
3 years ago
0
Tree by chromosome
#25
joshuak94
closed
3 years ago
1
Add benchmarking. large_file.bam is a large bam file of your choice, …
#24
joshuak94
closed
3 years ago
0
Reduce memory consumption when constructing the tree.
#23
joshuak94
closed
3 years ago
3
Reduce space
#22
joshuak94
closed
3 years ago
0
Overlap update
#21
MitraDarja
closed
3 years ago
0
New overlap
#20
MitraDarja
closed
3 years ago
0
Store offsets only
#19
joshuak94
closed
3 years ago
0
Add reading/writing of the interval tree via Cereal.
#18
joshuak94
closed
3 years ago
0
Look into alternative "FastStabbing" implementation.
#17
joshuak94
opened
3 years ago
0
For the CLI tool, create sub-argument parsers for indexing and searching.
#16
joshuak94
closed
3 years ago
1
Can we speed up the median calculation?
#15
joshuak94
opened
3 years ago
3
Store file offsets.
#14
joshuak94
closed
3 years ago
2
Update library structure
#13
joshuak94
closed
3 years ago
1
Parallelization?
#12
joshuak94
opened
3 years ago
2
Write and read the resulting interval tree.
#11
joshuak94
closed
3 years ago
0
Change mult chr
#10
joshuak94
closed
3 years ago
0
Small cleanups, including making relevant variables const, documentat…
#9
joshuak94
closed
3 years ago
0
Header conversion
#8
joshuak94
closed
3 years ago
0
Multiple chromosomes
#7
joshuak94
closed
3 years ago
0
Add api test
#6
MitraDarja
closed
3 years ago
0
Optimization fixes.
#5
joshuak94
closed
3 years ago
0
Overlap function
#4
MitraDarja
closed
3 years ago
0
Fix the printing.
#3
joshuak94
closed
3 years ago
0
[MISC] Add median to node and a get and set function
#2
MitraDarja
closed
3 years ago
0
Small optimization to construction.
#1
joshuak94
closed
3 years ago
0