Gert Hulselmans
Gert Hulselmans
Can an option (e.g. --keepcase) being added to mutfa to allow keeping the case of the reference nucleotide for the introduced mutation? FASTA file: ``` $ cat test.fa >seq1 AAAACCCCGGGGTTTT...
## Describe the feature request bashtop might have some interesting "widgets" that would look nice: https://github.com/aristocratos/bashtop For example the CPU section. With bottom on a node with 40 CPUs, the...
GTF file: ``` $ zcat ./test.gtf.gz chr21 hg19_knownGene exon 33026871 33027740 0.000000 - . gene_id "uc002yoz.1"; transcript_id "uc002yoz.1"; chr21 hg19_knownGene exon 33030247 33030540 0.000000 - . gene_id "uc002yoz.1"; transcript_id "uc002yoz.1";...
Make gzp usable as C library and/or python module For example, there is a python wrapper around [ISA-L](https://github.com/intel/isa-l)` which uses the `igzip` code to provide fast gzip decompression/compression (bad compression...
Add option to tabix to interleave multiple bgzipped indexed files, without the need for external resorting. ``` # bgzipped file*.bed.gz files with index. # "Concatenate" indexed bgzipped files so they...
Can some options of gzip be supported? gzip supports specifying options in `-cd` besides `-c -d: `-f` overwrites ouput instead of "compress with Z_FILTERED" `-q` surpresses warnings `--` for ending...
```python $ ../seq/seq-0.10.3/bin/seqc run test_backslach.seq ABC DEFGHI JKL ABC DEFGHI JKL $ ../seq/seq-0.11.0/bin/seqc run test_backslach.seq test_backslach.seq:7:15: error: syntax error, unexpected '\', expecting , , . $ cat test_backslach.seq s =...
It would be great if a `in_3.fastq` could be specified. A third FASTQ file is often used for single-cell ATAC data to indicate the cell barcode. This third read, is...
Crash when no signatures passed the filter: We ran into this issue with our NextFlow pipeline and a track database as a certain threshold was set to high, which caused...
```bash # Duc compiled with tokyo db backend. $ duc info -d /tmp/duc.tokyo.db Date Time Files Dirs Size Path 2019-07-02 19:22:34 18.6M 1.2M 47.8T /data # Duc compiled with kyoto...