Pierre Lindenbaum

Problem with arity=2: and argument containing '{}[]:' characters

2

Hi, Sorry if it's a known bug or if I'm missing someting. Here is my test file below: Arity is 2. It bugs when the VALUE contains a json string....

If I'm not wrong in https://github.com/cbeust/jcommander/blob/master/src/main/java/com/beust/jcommander/JCommander.java#L652 ``` if (descriptions.containsKey(name)) { ``` description is a` Map and it's compared to a `String`. the implementations of IKey.equals in StringKey or ProgramName don't...

Suggestions : paths ; case/control

3

Hi Brent , here are two suggestions for indexcov - using a file containing the path to the bams (to avoid something like `xargs` ) - if we could include...

Feature Request: recursive process

9

## New feature as seen on twitter https://twitter.com/yokofakun/status/1248533372630155264 I'd like to have a way to describe a **recursive** process that would call itself until a condition is done. I have...

sort published files so common bioinformatics indexes are processed at the end.

2

Hi, this small PR is related to the following issue: https://github.com/nextflow-io/nextflow/issues/1489 When publishing a set of paths, reorder the files so the common indexes (TBI, BAI,CSI...) are copied at the...

fix sqrt(VarQ) when VarQ<=0

1

Hi this PR is a possible fix for https://github.com/zhanxw/rvtests/issues/133 . But I'm not sure if it's the correct way to do it. Thanks.

SKATO: rvtest frozen/stalled (3 variants) (minimal example provided)

1

Hi, find in attachement where rvtest seems stalled/frozen (skato test ?) while there is a small number of variant. ``` $ unzip -l test.zip Archive: test.zip Length Date Time Name...

'setFile' format 0-based or 1-based ? refFlat: only exons ?

1

Hi, thank your for writing rvtests. A quick question: if the `setFile` format - half-closed 0-based like bed ? - or open 1-based like gtf/gff ? And in the refFlat...

As seen on twitter : https://twitter.com/nilshomer/status/1283413286684258305 . Unless I'm wrong ( seq->name.l is outdated ?) changing: int t = strlen(p->name); to int t = seq->name.l should be faster.

sam_format1 : replace if/then with switch/case

1

some minor optimizations : in `sam.c / sam_format1` I replaced the successions of `if/then` with `switch/case`. replaced the `goto` with a macro. I also fixed a | FIXME` in the...