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pdimens
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harpy
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
https://pdimens.github.io/harpy
GNU General Public License v3.0
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convert circlize + plotly to BioCircos
#111
pdimens
closed
3 months ago
0
Svplots
#110
pdimens
closed
3 months ago
0
[SV] interactive variant plots as single plots with dropdowns
#109
pdimens
closed
3 months ago
1
rm ggplot and ggridges code
#108
pdimens
closed
3 months ago
0
[phase] ridgeplot replacement
#107
pdimens
closed
3 months ago
0
[phase] retain sites with less than or more than 2 alleles
#106
pdimens
closed
3 months ago
0
[phase] --vcf-samples not working correctly
#105
pdimens
closed
3 months ago
1
[phase] --genome error
#104
pdimens
closed
3 months ago
1
Deconvolute
#103
pdimens
closed
4 months ago
0
Deconvolute
#102
pdimens
closed
4 months ago
0
100 impute create separate conda env for stitch
#101
pdimens
closed
4 months ago
0
[IMPUTE] create separate conda env for STITCH
#100
pdimens
closed
4 months ago
1
alphabetize workflow options
#99
pdimens
closed
4 months ago
0
[QC] --skip-adapters should be opt-in as --trim-adapters
#98
pdimens
closed
4 months ago
0
[QC] add deduplication to fastp
#97
pdimens
closed
4 months ago
0
[internal] replace --print-only with --config-only
#96
pdimens
closed
4 months ago
0
Docs 1.1
#95
pdimens
closed
4 months ago
0
replace molecule distance with QuickDeconvolute?
#94
pdimens
closed
4 months ago
0
move pysam into main env
#93
pdimens
closed
4 months ago
0
Add aggregate report for bx stats
#92
pdimens
closed
4 months ago
0
add pysam as direct dependency
#91
pdimens
closed
4 months ago
0
replace minimap with strobealign
#90
pdimens
closed
4 months ago
0
replace minimap with strobealign
#89
pdimens
closed
4 months ago
0
new input model listing abspaths in config.yaml
#88
pdimens
closed
4 months ago
0
(harpy align) - aggregate report for BX stats for all samples
#87
pdimens
closed
4 months ago
0
harpy hpc to create executor plugin templates
#86
pdimens
closed
4 months ago
0
remove need for workflow/input
#85
pdimens
closed
4 months ago
0
add manual rerun
#84
pdimens
closed
4 months ago
1
add HPC subcommand and support
#83
pdimens
closed
5 months ago
0
update to 1.0
#82
pdimens
closed
5 months ago
0
begin 1.0 migration
#81
pdimens
closed
5 months ago
0
consider phasing with whatshapp haplotagphase
#80
pdimens
closed
5 months ago
1
molecule coverage
#79
pdimens
closed
5 months ago
0
change alignment depth to use samtools depth
#78
pdimens
closed
5 months ago
1
Singularity
#77
pdimens
closed
6 months ago
0
add simulate linkedreads
#76
pdimens
closed
6 months ago
0
replace snp windowsize with regions
#75
pdimens
closed
6 months ago
0
rebase docs_dev
#74
pdimens
closed
6 months ago
0
internal API overhaul
#73
pdimens
closed
6 months ago
0
internal API overhaul
#72
pdimens
closed
6 months ago
0
Add bam indexing to snp module
#71
pdimens
closed
6 months ago
1
Update snp.md to specify indexed bam files required as input
#70
gmkov
closed
6 months ago
2
Update wiki to ensure module names are consistent
#69
gmkov
closed
6 months ago
1
harpy impute error IsADirectoryError:
#68
gmkov
opened
6 months ago
63
make all the mermaids nicer
#67
pdimens
closed
7 months ago
0
update to 0.9x
#66
pdimens
closed
7 months ago
0
fix adapter flag for qc
#65
pdimens
closed
7 months ago
0
Merge pull request #59 from pdimens/docs_dev
#64
pdimens
closed
7 months ago
0
stage release of version 0.9
#63
pdimens
closed
7 months ago
0
-x for module `qc` creates error
#62
pdimens
closed
7 months ago
0
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