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quinlan-lab
/
STRling
Detect novel (and reference) STR expansions from short-read data
MIT License
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Fragment bounds
#72
brentp
closed
4 years ago
0
v0.3.0 release candidate
#71
hdashnow
closed
4 years ago
0
Fix int overflow bug
#70
hdashnow
closed
4 years ago
0
strling merge: reduce memory usage
#69
brentp
closed
4 years ago
2
WIP: reduce memory use
#68
brentp
closed
4 years ago
0
WIP:reduce memory use in merge
#67
brentp
closed
4 years ago
1
[WIP] Per sample cluster
#66
hdashnow
closed
4 years ago
1
require min reads in at least one sample during merge clustering
#65
brentp
closed
4 years ago
0
Index
#64
hdashnow
closed
4 years ago
1
Parsing issue with outliers.py
#63
jgunti-code
closed
3 years ago
4
Support hemizygous calls in males on sex chromosomes
#62
hdashnow
opened
4 years ago
0
Docs updates for 0.2.1
#61
hdashnow
closed
4 years ago
0
Version 0.2.1 candidate, with bed parsing fix
#60
hdashnow
closed
4 years ago
0
Address input bed file bugs
#59
hdashnow
closed
4 years ago
0
STRling merge error "SIGSEGV: Illegal storage access" when -l bed is used
#58
hdashnow
closed
4 years ago
0
Candidate for release v0.2.0 - fixed merge conflicts
#57
hdashnow
closed
4 years ago
0
Candidate for release v0.2.0
#56
hdashnow
closed
4 years ago
1
Fpr
#55
brentp
closed
4 years ago
6
Need a more useful error for when bed file chromosomes don't match reference genome
#54
hdashnow
opened
4 years ago
0
Homopolymer false positives
#53
hdashnow
closed
4 years ago
11
Do some sensible filtering by default
#52
hdashnow
opened
4 years ago
0
Spanning fragment calculations rebased on dev branch
#51
hdashnow
closed
4 years ago
0
Limit allocation of unplaced reads to larger alleles
#50
hdashnow
closed
4 years ago
0
Outlier analysis in Python
#49
hdashnow
closed
3 years ago
0
Update random simulations
#48
hdashnow
closed
4 years ago
0
DO NOT MERGE: proper simulations
#47
brentp
opened
4 years ago
0
[WIP] Pipelines
#46
hdashnow
closed
4 years ago
0
Clean up docs, esp. in README
#45
hdashnow
closed
4 years ago
0
Report number of anchored reads
#44
hdashnow
closed
4 years ago
0
align_length > 0 Assertion Error
#43
christopher-schroeder
closed
3 years ago
3
Docs
#42
hdashnow
closed
4 years ago
0
[WIP] individual and joint calling bpipe pipelines for cram or bam
#41
hdashnow
closed
4 years ago
1
DO NOT MERGE: branch for using bootstrap sims to estimate std dev of size estimate
#40
brentp
closed
4 years ago
0
update to work with htslib 1.10+
#39
brentp
closed
4 years ago
3
Typo and bug in the version warning?
#38
hdashnow
closed
3 years ago
1
add sphinx documentation
#37
hdashnow
closed
4 years ago
0
Joint genotyping
#36
hdashnow
closed
4 years ago
0
assign_reads_locus produces bad indices
#35
hdashnow
closed
4 years ago
2
STRling version number is in two places
#34
hdashnow
opened
4 years ago
0
Check versions of htslib and hts.nim
#33
hdashnow
closed
3 years ago
1
Call stage has high memory utilization for large numbers of bounds
#32
hdashnow
closed
4 years ago
1
Merge
#31
hdashnow
closed
4 years ago
2
merge
#30
hdashnow
closed
4 years ago
1
Adjust adjust by
#29
brentp
closed
4 years ago
0
Output bam file with relocated anchored STR mates
#28
hdashnow
closed
3 years ago
1
add none_left, none_right
#27
brentp
closed
4 years ago
2
Error: repeat not found in expected region
#26
danielecook
closed
3 years ago
8
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
#25
bjtrost
closed
3 years ago
6
Add a sample input file
#24
hdashnow
closed
4 years ago
1
remove requirement for softclipped reads on each side
#23
hdashnow
closed
4 years ago
0
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