luederm

Issues with Circular Layout

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Hello, I am having a couple issues with the circular layout and I was wondering if there is a way around them. **Issue 1) Semicircle trees have lots of unnecessary...

Resolves #568. Changes: 1) Remove excess whitespace in semicircle layouts. ``` from ete3 import Tree, TreeStyle t = Tree() t.populate(30) ts = TreeStyle() ts.show_leaf_name = True ts.mode = "c" ts.arc_start...

Billiard is leaving pipes open

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I am using Celery to initiate long running pipelines and I override multiprocessing imports with Biliard. I notice as a pipeline runs, the number of open files (pipes) steadly increases...

Spades is printing errors to stdout

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### Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above. Spades prints errors not caught by argparse to...

Hello, I am running the latest gencore with --no_duplex and -s = 3. However, I am still getting many reads output which have the same UMI and identical mapping coordinates....

Hello, After deduplicating with gencore I am getting a number of errors with GATK's ValidateSamFile: - ERROR::MISMATCH_MATE_ALIGNMENT_START, Mate alignment does not match alignment start of mate - ERROR::MISMATCH_FLAG_MATE_NEG_STRAND, Mate negative...

SEQC2: Some high confidence SNVs and INDELs in VCF are outside of regions defined by High-Confidence_Regions_v1.2.bed

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I downloaded high-confidence_sINDEL_in_HC_regions_v1.2.vcf.gz and high-confidence_sINDEL_in_HC_regions_v1.2.vcf.gz from FTP but noticed that some of the variants are not in the regions defined by High-Confidence_Regions_v1.2.bed. This led to issues when I compared my...

I often use vcfpy to create VCF files from non-vcf data sources, such as a spreadsheet. One difficulty with doing this has been creating AltRecords for alternative alleles. Looking through...