profile
viewpoint
If you are wondering where the data of this site comes from, please visit https://api.github.com/users/jtal/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.

philipkimmey/GSC-Hudson 6

Washington University Genome Center Hudson testing suite and deploy scripts

jtal/Seqmon 2

Seqmon

genomejim/fsft 1

Fantastic Science Force Tactics

jtal/BuildYourOwnLisp 0

Learn C and build your own programming language in under 1000 lines of code!

jtal/ember_rails 0

Very simple emberjs app

jtal/HRS-Parser 0

A recursive descent parser to extract citations from Hawaii Revised Statues in order to link directly to the relevant document.

jtal/kc 0

Kuali Coeus

jtal/kuali_kc 0

Kuali Coeus

jtal/photography 0

A jekyll website for photographers

delete branch pac4j/play-pac4j

delete branch : renovate/mockito.version

delete time in 4 days

push eventpac4j/play-pac4j

renovate[bot]

commit sha f42867514f820e565ec5f79bce79ddaf2eb95294

Update dependency org.mockito:mockito-core to v3.10.0 (#405) Co-authored-by: Renovate Bot <bot@renovateapp.com>

view details

push time in 4 days

PR merged pac4j/play-pac4j

Update dependency org.mockito:mockito-core to v3.10.0

WhiteSource Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
org.mockito:mockito-core 3.9.0 -> 3.10.0 age adoption passing confidence

Configuration

📅 Schedule: At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻️ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.


  • [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box.

This PR has been generated by WhiteSource Renovate. View repository job log here.

+1 -1

0 comment

1 changed file

renovate[bot]

pr closed time in 4 days

PR opened pac4j/play-pac4j

Update dependency org.mockito:mockito-core to v3.10.0

WhiteSource Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
org.mockito:mockito-core 3.9.0 -> 3.10.0 age adoption passing confidence

Configuration

📅 Schedule: At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻️ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.


  • [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box.

This PR has been generated by WhiteSource Renovate. View repository job log here.

+1 -1

0 comment

1 changed file

pr created time in 4 days

create barnchpac4j/play-pac4j

branch : renovate/mockito.version

created branch time in 4 days

MemberEvent

issue openedgenome/bam-readcount

fpfilter.pl - failed to get readcounts for variant allele

I'm new to variant calling and I'm having trouble running VarScan2 v2.4.4 (Support Protocol 1) which can be found in the following online document: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278659 /

The authors advise using the fpfilter.pl accessory script (https://sourceforge.net/projects/varscan/files/scripts/). When I run the following command:

perl script_FPfilter sample.varScan.snp.filter.bed varScan.variants.readcounts –output-basename varScan.variants.filter

I get the following output:

27841 variants 27841 failed to get readcounts for variant allele 0 had read position < 0.1 0 had strandedness < 0.01 0 had var_count < 4 0 had var_freq < 0.05 0 had mismatch qualsum difference > 50 0 had mapping quality difference > 30 0 had read length difference > 25 0 had var_distance_to_3' < 0.2 0 passed the strand filter

Apparently, the problem is with obtaining the readcounts.

The bam-readcounts files were obtained as follows:

create indexed bam files samtools index bqsr_output.bam

create bed file for sample.varScan.snp.filter vcf2bed --snvs sample.varScan.snp.filter > sample.varScan.snp.filter.bed

run bam-read-count bam-readcount -q 1 -b 20 -f hg38_genome.fa -l sample.varScan.snp.filter.bed bqsr_output.bam > snp_varScan.variants.readcounts

what am I doing wrong?

created time in 5 days

delete branch pac4j/play-pac4j

delete branch : renovate/org.apache.maven.plugins-maven-gpg-plugin-3.x

delete time in 6 days

push eventpac4j/play-pac4j

renovate[bot]

commit sha cf8071a5ae5ccb632dd84632484ccef0f66b7d8a

Update dependency org.apache.maven.plugins:maven-gpg-plugin to v3 (#404) Co-authored-by: Renovate Bot <bot@renovateapp.com>

view details

push time in 6 days

PR merged pac4j/play-pac4j

Update dependency org.apache.maven.plugins:maven-gpg-plugin to v3

WhiteSource Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
org.apache.maven.plugins:maven-gpg-plugin 1.6 -> 3.0.1 age adoption passing confidence

Configuration

📅 Schedule: At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻️ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.


  • [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box.

This PR has been generated by WhiteSource Renovate. View repository job log here.

+1 -1

0 comment

1 changed file

renovate[bot]

pr closed time in 6 days

PR opened pac4j/play-pac4j

Update dependency org.apache.maven.plugins:maven-gpg-plugin to v3

WhiteSource Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
org.apache.maven.plugins:maven-gpg-plugin 1.6 -> 3.0.1 age adoption passing confidence

Configuration

📅 Schedule: At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻️ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.


  • [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box.

This PR has been generated by WhiteSource Renovate. View repository job log here.

+1 -1

0 comment

1 changed file

pr created time in 7 days

issue closedgenome/bam-readcount

Fail to open BAM file –q

I'm running the False Positive Filter recommended in Support Protocol 1 by Koboldt et al (2013) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278659/). The recommendations are:

Obtain metrics for the list of variants:

bam-readcount –q 1 –b 20 –f reference.fasta –l varScan.variants BAM_FILE> varScan.variants.readcounts

When trying to perform the command line:

bam-readcount –q 1 –b 20 –f hg38_genome.fa –l sample.varScan.snp.filter bqsr_output.bam> varScan.variants.readcounts

I get the following output:

Minimum mapping quality is set to 0 open: No such file or directory Fail to open BAM file –q

I consulted some guidelines and it was suggested that the varScan.variants file should be in bed format. I made the following attempts:

vcf2bed <sample.varScan.snp.filter> varScan.variants.bed

awk '$ 1 ~ / ^ # / {next} {print $ 1, $ 2-1, $ 2}' sample.varScan.snp.filter | sort -k1,1 -k2,2n -u> filter_out.bed

But in both attempts the exit was:

Minimum mapping quality is set to 0 open: No such file or directory Fail to open BAM file –q

As recommended in the article it is suggested that "A list of variants (SNVs or indels) in VarScan format (tab-delimited; the first five columns must be chromosome, position, reference allele, variant allele)".

So, I also tried:

awk -F '\ t' '{print $ 1, $ 2, $ 4, $ 5, $ 3, $ 6, $ 7, $ 8, $ 9, $ 10}' sample.varScan.snp.filter> snp_filter_out.bed

And the failure remained.

What's wrong?

[bam-readcount version: 0.8.0]

closed time in 9 days

Souzavgp

issue commentgenome/bam-readcount

Fail to open BAM file –q

Awesome. Closing this issue.

Souzavgp

comment created time in 9 days

issue commentgenome/bam-readcount

Fail to open BAM file –q

It looks to me like you're using a long-dash (also called em-dash) when specifying your parameters instead of a normal dash (minus sign). The parsers is not interpreting the –q as an option but as a string and thinks that that is the path to your bam file. Please replace the em-dashes in your bam-readcount commands with simple dashes e.g. -q.

Hello Susannasiebert, your observation is correct.

Thank you.

Souzavgp

comment created time in 9 days

issue commentgenome/bam-readcount

Fail to open BAM file –q

Parece-me que você está usando um traço longo (também chamado de travessão) ao especificar seus parâmetros em vez de um traço normal (sinal de menos). O analisador não está interpretando o –qcomo uma opção, mas como uma string e pensa que esse é o caminho para o seu arquivo bam. Substitua os travessões em seus comandos bam-readcount por travessões simples, por exemplo -q.

Hello Susannasiebert, your observation is correct.

Thank you.

Souzavgp

comment created time in 9 days

issue commentgenome/bam-readcount

Fail to open BAM file –q

It looks to me like you're using a long-dash (also called em-dash) when specifying your parameters instead of a normal dash (minus sign). The parsers is not interpreting the –q as an option but as a string and thinks that that is the path to your bam file. Please replace the em-dashes in your bam-readcount commands with simple dashes e.g. -q.

Souzavgp

comment created time in 9 days

issue openedgenome/bam-readcount

Fail to open BAM file –q

I'm running the False Positive Filter recommended in Support Protocol 1 by Koboldt et al (2013) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278659/). The recommendations are:

Obtain metrics for the list of variants:

bam-readcount –q 1 –b 20 –f reference.fasta –l varScan.variants BAM_FILE> varScan.variants.readcounts

When trying to perform the command line:

bam-readcount –q 1 –b 20 –f hg38_genome.fa –l sample.varScan.snp.filter bqsr_output.bam> varScan.variants.readcounts

I get the following output:

Minimum mapping quality is set to 0 open: No such file or directory Fail to open BAM file –q

I consulted some guidelines and it was suggested that the varScan.variants file should be in bed format. I made the following attempts:

vcf2bed <sample.varScan.snp.filter> varScan.variants.bed

awk '$ 1 ~ / ^ # / {next} {print $ 1, $ 2-1, $ 2}' sample.varScan.snp.filter | sort -k1,1 -k2,2n -u> filter_out.bed

But in both attempts the exit was:

Minimum mapping quality is set to 0 open: No such file or directory Fail to open BAM file –q

As recommended in the article it is suggested that "A list of variants (SNVs or indels) in VarScan format (tab-delimited; the first five columns must be chromosome, position, reference allele, variant allele)".

So, I also tried:

awk -F '\ t' '{print $ 1, $ 2, $ 4, $ 5, $ 3, $ 6, $ 7, $ 8, $ 9, $ 10}' sample.varScan.snp.filter> snp_filter_out.bed

And the failure remained.

What's wrong?

[bam-readcount version: 0.8.0]

created time in 9 days

delete branch pac4j/play-pac4j

delete branch : renovate/net.alchim31.maven-scala-maven-plugin-4.x

delete time in 13 days

push eventpac4j/play-pac4j

renovate[bot]

commit sha 7cae57a793be5d9feac281ba2f7de9a108c6dc18

Update dependency net.alchim31.maven:scala-maven-plugin to v4.5.1 (#403) Co-authored-by: Renovate Bot <bot@renovateapp.com>

view details

push time in 13 days

PR merged pac4j/play-pac4j

Update dependency net.alchim31.maven:scala-maven-plugin to v4.5.1

WhiteSource Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
net.alchim31.maven:scala-maven-plugin 4.4.1 -> 4.5.1 age adoption passing confidence

Configuration

:date: Schedule: At any time (no schedule defined).

:vertical_traffic_light: Automerge: Disabled by config. Please merge this manually once you are satisfied.

:recycle: Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

:no_bell: Ignore: Close this PR and you won't be reminded about this update again.


  • [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box.

This PR has been generated by WhiteSource Renovate. View repository job log here.

+1 -1

0 comment

1 changed file

renovate[bot]

pr closed time in 13 days

push eventpac4j/play-pac4j

Renovate Bot

commit sha 43b8a42628addbe46cff95cc5f70b43ca440ad75

Update dependency net.alchim31.maven:scala-maven-plugin to v4.5.1

view details

push time in 13 days

PR opened pac4j/play-pac4j

Update dependency net.alchim31.maven:scala-maven-plugin to v4.5.0

WhiteSource Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
net.alchim31.maven:scala-maven-plugin 4.4.1 -> 4.5.0 age adoption passing confidence

Configuration

:date: Schedule: At any time (no schedule defined).

:vertical_traffic_light: Automerge: Disabled by config. Please merge this manually once you are satisfied.

:recycle: Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

:no_bell: Ignore: Close this PR and you won't be reminded about this update again.


  • [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box.

This PR has been generated by WhiteSource Renovate. View repository job log here.

+1 -1

0 comment

1 changed file

pr created time in 13 days

issue openedJam3/math-as-code

Is this project abandoned?

created time in 16 days

issue openeddgidb/dgidb

Consider CanSar database as a source of interactions

Example result: https://cansarblack.icr.ac.uk/target/P15056/synopsis/ligandability

Terms of use may make integration of this source impossible... investigate further.

created time in 18 days

PR closed spring-guides/gs-serving-web-content

Adding namespace for resolving Thymeleaf in HTML

Hi,

Noticed that unless you add namespace in greetings.html. It just prints out "greeting".

+13 -0

3 comments

1 changed file

abhishek-galoda

pr closed time in 18 days

delete branch spring-guides/gs-serving-web-content

delete branch : master

delete time in 18 days

pull request commentspring-guides/gs-serving-web-content

Adding namespace for resolving Thymeleaf in HTML

@abhishek-galoda Thank you for signing the Contributor License Agreement!

abhishek-galoda

comment created time in 18 days

create barnchspring-guides/gs-serving-web-content

branch : main

created branch time in 18 days