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maize-genetics
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phg_v2
PHG version 2
https://phg.maizegenetics.net/
Apache License 2.0
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Removing the option to have map-kmers hit multiple reference ranges.
#217
zrm22
opened
2 days ago
1
Updates to build_and_load.md Quick Start
#216
tcasstevens
closed
2 days ago
1
verify AGC files bug fix
#215
lynnjo
closed
1 week ago
1
Add reference file path
#214
btmonier
closed
1 week ago
0
Fix "Quick Start" parameters
#213
btmonier
closed
1 week ago
0
Create fasta from hvcf fix duplicate entries
#212
lynnjo
closed
2 weeks ago
1
Add PHG version retrieval method
#211
btmonier
closed
2 weeks ago
1
Add call-out for `create-ranges` command
#210
btmonier
closed
3 weeks ago
0
Try removing all references to obligatory conda environment
#209
dirkjanvw
opened
3 weeks ago
0
[REQUEST]: allow non-conda installation of dependencies
#208
dirkjanvw
closed
3 weeks ago
10
Handling gzipped file names correctly now. Also adding in a helper f…
#206
zrm22
closed
3 weeks ago
1
[BUG]: map-kmers does not fully strip file extension that includes .gz suffix
#205
matthewwiese
closed
3 weeks ago
3
change CliktCommands to use required() for required parameters
#204
tcasstevens
closed
1 month ago
3
Update maf to gvcf
#203
zrm22
closed
1 month ago
1
General typo fixes
#202
btmonier
closed
1 month ago
0
Hvcf2gvcf ref allele wrong
#201
lynnjo
closed
1 month ago
1
Update `setup-environment` docs
#199
btmonier
closed
1 month ago
0
Setup env file not exist
#198
tcasstevens
closed
1 month ago
1
Fix list appearance in export docs
#197
btmonier
closed
1 month ago
0
Fixing Build Kmer Index Diagnostic Error.
#196
zrm22
closed
1 month ago
1
update docs for create-fasta-from-hvcf to match code changes
#195
lynnjo
closed
1 month ago
0
add condaEnvPrefix to Gvcf2hvcf and places it is called
#194
lynnjo
closed
1 month ago
1
Add "Convenience Command" docs
#193
btmonier
closed
1 month ago
0
Out of memory problem while creating fasta from hvcf
#191
sidevshiy
opened
1 month ago
4
Speedup map kmers
#190
zrm22
closed
1 month ago
1
Mapping Paired-End Reads with PHG Takes Too Long
#187
sidevshiy
closed
1 month ago
12
Merge hvcf file hvcf dir create fasta from hvcf
#186
lynnjo
closed
1 month ago
1
Fix site background and installation steps
#185
btmonier
closed
1 month ago
0
added PrepareSlurmAlignFile to Phg.kt
#184
lynnjo
closed
1 month ago
1
[BUG]: There is no command in phg prepare-slurm-align-file
#183
sidevshiy
closed
1 month ago
3
Multiple file bug create fasta from hcvcf
#182
lynnjo
closed
1 month ago
1
Fix formatting issues with mkdocs
#181
btmonier
closed
1 month ago
0
Update landing page
#180
btmonier
closed
1 month ago
1
Add CNAME
#179
btmonier
closed
1 month ago
0
Update site URL
#178
btmonier
closed
1 month ago
0
Fixed pulling chrom name from fasta idLine
#177
lynnjo
closed
1 month ago
1
Fix "Build and Load" quick-start parameters
#176
btmonier
closed
1 month ago
0
Initial framework for site generation
#175
btmonier
closed
2 months ago
0
Multi ref range read mapping
#174
zrm22
closed
1 month ago
1
Gvcf from hvcf
#173
lynnjo
closed
1 month ago
1
Add SLURM usage sections
#172
btmonier
closed
2 months ago
0
Merge gvcfs clikt command
#170
tcasstevens
closed
2 months ago
2
Refactor alignassemblies
#169
lynnjo
closed
3 months ago
1
Ktor/BrAPI specifications
#168
btmonier
closed
3 months ago
0
chnages to include condaEnvPrefix for all ProcessBuilder calls
#167
lynnjo
closed
3 months ago
1
Update export command usage
#166
btmonier
closed
3 months ago
0
Rearrange doc sections in "Build and Load"
#165
btmonier
closed
3 months ago
0
Kmer index allow span ref range
#163
zrm22
closed
3 months ago
1
Documentation - Add "QC Metrics" section
#162
btmonier
closed
3 months ago
0
Fix build kmer index chromosome naming
#161
pjbradbury
closed
3 months ago
1
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