lindenb jvarkit issues - Githubissues

lindenb / jvarkit

Java utilities for Bioinformatics

https://jvarkit.readthedocs.io/

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installation issue

#201 newatil opened 2 years ago
1
biostar154220 removes too many reads when using with a bed file

#200 sbrohee closed 2 years ago
2
[INFO][WGSCoveragePlotter]no valid chromosome was found in

#199 jolvany closed 2 years ago
1
fixvcfmissinggenotypes.jar does not actually fix missing genotypes

#198 Giuseppe1995 closed 2 years ago
2
Launcher unable to close index

#197 DcornishUCL closed 2 years ago
3
Adding INFO data in bioalcidaejdk.jar result

#196 se2cheeese opened 2 years ago
1
Task 'gephicmd' not found in root project 'jvarkit'

#195 yangzuokun closed 2 years ago
1
Improve GRADLE build Performance

#194 shisheng-1 closed 2 years ago
1
Added an option to ignore N bases in reads, which can lead to much cl…

#193 yfarjoun closed 2 years ago
1
found non-ASCII code after verticalGridLinesVisible in XYPlot.java

#192 lijingbu closed 1 year ago
2
counts variant consequences per gene

#191 Kaskere closed 2 years ago
1
sam2tsv lists incorrect reference sequence & positions

#190 dchakro closed 2 years ago
11
set seed for biostar145820.jar

#189 sklasfeld opened 2 years ago
1
tview / ttview equivalent for protein-peptides bam

#188 avilella opened 2 years ago
1
sam2tsv question: any way to only parse reads that overlap specific coordinates in reference?

#187 hengjwj closed 2 years ago
2
Same version of java also fails

#186 Alqueno opened 2 years ago
1
Settings.gradle empty

#185 AndModica closed 2 years ago
1
Failed to build biostar145820 (Build file '/jvarkit/build.gradle' line: 676)

#184 gilhornung closed 3 months ago
1
WGSCoveragePlotter: Illegal Capacity: -4

#183 aaronphillips7493 closed 1 year ago
3
Sam2Tsv --regions option not working

#182 MiHern closed 3 years ago
6
Cannot use .fna reference file

#181 togop closed 3 years ago
2
findallcoverageatposition output incorrect numbers

#180 yliueagle opened 3 years ago
5
number of aligned reads inconsistency between sam2tsv and samtools mpileup

#179 Huanle closed 3 years ago
2
When AF=1, not all positions have changed

#178 LauraVP1994 closed 3 years ago
8
Clarify use of `--samples` and `--partition` in WGSCoveragePlotter

#177 pvanheus closed 3 years ago
8
Gtf file with NCBI Ids for backlocate

#176 pawarad closed 1 year ago
4
Actual AF vs target AF in Introducing artificial mutation SNV in bam (biostar404363)

#175 ericaenjoy3 opened 3 years ago
0
Are there default filters in sam2tsv? (general question; not an issue)

#174 kac2053 closed 5 months ago
1
MantaMerger running time too long and potential speeding up methods?

#173 zjgbz closed 5 months ago
2
central maven error

#172 PhilliVanilli closed 3 years ago
2
gridsspostprocessvcf estimates Breakpoint INS like DEL.

#171 gmgs-999 closed 3 years ago
1
backlocate does not work

#170 pawarad closed 3 years ago
3
java.lang.RuntimeException: Not a diploid organism.

#169 CornilleAmandine closed 5 months ago
2
Couldn't open vcffilterjdk.jar

#168 ASQWZXED closed 3 years ago
11
Could not initialize class org.codehaus.groovy.runtime.InvokerHelper

#167 ASQWZXED closed 3 years ago
2
sam2tsv doesn't report chrX, Y, M reads

#166 kac2053 closed 3 years ago
12
vcfpolyx counts homopolymer repeats in the wrong position

#165 ftucos closed 3 years ago
3
Vcf2Bam not recognizing sequence dictionary

#164 Mahmoudy96 closed 5 months ago
4
include sam2tsv as a third party software

#163 Huanle opened 3 years ago
0
Backlocate transcript not found

#162 esamorodnitsky closed 4 years ago
6
sam2tsv makes extraordinarily large files

#161 jasvinderahuja closed 4 years ago
2
Extract only the portion of read overlapping to bed

#160 MaestSi closed 4 years ago
2
sam2tsv

#159 mohammedmsk closed 4 years ago
2
Biostar398854 does not work

#158 AlBaarS opened 4 years ago
1
issue with providing filter options

#157 hudenise2 closed 4 years ago
9
Depth of fixed genotypes seems incorrect

#156 RNieuwenhuis closed 4 years ago
4
Not working with VCFs that have multiple chromosomes.

#155 bambrozio opened 4 years ago
7
SamViewWithMate: width one regions using BED file

#154 daynefiler closed 4 years ago
2
[FixVcfMissingGenotypes]partial missing values for GL field, Ignoring SAM validation error, and [Launcher]fixvcfmissinggenotypes Exited with failure (-1)

#153 jdalapicolla closed 4 years ago
4
Add -a,--all option to cmpbams so it compares all reads

#152 lckarssen closed 4 years ago
2

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