seppinho haplogrep-cmd issues

seppinho / haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

https://haplogrep.i-med.ac.at/

MIT License

73 stars 23 forks source link

issues

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Phylotree

#52 rohandavidg opened 1 year ago
0
Enhancement: Calculate Mutation Burden

#51 DarioS opened 1 year ago
0
Errors if Whole Genome VCF Input

#50 DarioS opened 1 year ago
0
--rsrs option crashes

#49 JoshuaDanielRubin opened 2 years ago
4
how get the sample quality and HG quality using command line haplogrep

#48 rarahmati opened 2 years ago
0
java.nio.file.DirectoryNotEmptyException

#47 WZo0o closed 1 year ago
2
Return correct exit code

#46 lukfor closed 2 years ago
1
Haplogrep error with a vcf-merge file.

#45 VGDEC opened 2 years ago
1
Update code formatting

#44 lukfor closed 2 years ago
1
can't install haplogrep-cmd

#43 kopelol closed 2 years ago
5
haplogrep on non-human species

#42 leleory opened 3 years ago
1
Installation not working

#41 divonlan closed 2 years ago
1
Issues with processing indels in VCF

#40 shadrinams opened 3 years ago
1
Bug #38 Add tarLongFileMode to pom.xml to allow big user IDs

#39 david-ma closed 2 years ago
2
Bug: Fails to build when user ID is too big. Add tarLongFileMode to pom.xml

#38 david-ma closed 2 years ago
1
Quality ∞% ?

#37 Alessio0796 opened 3 years ago
4
add fasta export for console version

#36 haansi closed 2 years ago
1
Haplogroup Quality score >1？

#35 nanshanjin opened 4 years ago
5
input file error on 2.2.0

#34 jamigo closed 4 years ago
4
Remove jbwa-xxxx folder after running HaploGrep

#33 alexhbnr closed 4 years ago
4
Microarrays and missing data, `--chip`

#32 stephenturner opened 4 years ago
0
Feature request: least common ancestor for equally scoring haplogroups

#31 stephenturner opened 4 years ago
4
MicroArrays and back-mutations

#30 haansi opened 4 years ago
0
Is the XML file mal-formatted?

#29 mocksu closed 4 years ago
12
Error on output on 'Not Found' variants

#28 nuin closed 5 years ago
1
Export FASTA using the command line version

#27 teepean opened 5 years ago
1
Heteroplasmic insertion

#26 haansi closed 5 years ago
1
Add alignment rules to place indels correctly

#25 seppinho closed 5 years ago
1
Bug on running haplogrep on windows

#24 elffuos closed 5 years ago
2
pom.xml warning: jdom is written twice and doesn't correspond to dependency org.jdom:jdom:*:*

#23 monkollek closed 5 years ago
0
pom.xml error. incorrect paths for resources: phylotree, weights and annotation

#22 monkollek closed 5 years ago
0
Running HaploGrep v2.1.18on MacOS

#21 elffuos closed 5 years ago
1
Allow FastA file extension other than "fasta"?

#20 alexhbnr closed 5 years ago
1
bump version number

#19 stephenturner closed 5 years ago
0
Fix MacOS issue for FASTA

#18 seppinho closed 5 years ago
15
Add Contamination Simulator

#17 haansi closed 5 years ago
1
FASTA failure - missing file

#16 sushilashenoy closed 5 years ago
6
Add test-cases for RSRS

#15 haansi opened 5 years ago
0
Feature fasta

#14 seppinho closed 5 years ago
0
Add recombination feature in console version

#13 haansi closed 2 years ago
0
Allow export of first-n best haplogroups

#12 haansi closed 5 years ago
7
Extra space on columns when --extend-report is used

#11 nuin closed 5 years ago
0
Error when using --lineage option

#10 nuin closed 5 years ago
13
Start Classification... java.lang.NumberFormatException: For input string: "15940*"

#9 snashraf closed 5 years ago
8
Error message for non-haploid genotypes in vcf

#8 haansi closed 6 years ago
0
Provide a Haplogrep RSRS Version

#7 seppinho closed 6 years ago
2
Annotate FASTA file

#6 nuin closed 6 years ago
4
Error - cannot find input file haplogrep 2.1.8

#5 jayaramanp closed 6 years ago
0
Recheck backmutations in remaining polymorphisms

#4 haansi opened 6 years ago
0
Support Fasta

#3 seppinho closed 5 years ago
0