Gert Hulselmans

samtools query (similar to bcftools query): Write user defined output from BAM files or write calculated expressions to tags

1

#### Is your feature request related to a problem? Please specify. It would be nice to have a `samtools query` command (similar to `bcftools query`) (other name is fine too),...

Mention somewhere that multiallelic variants need to be expanded with e.g. `bcftools norm --multiallelics +both`, if you want to remove overlaps with `bcftools +remove-overlaps`. An entry that contain multiple mutations...

"hq server info --stats" does not show values.

1

`hq server info --stats` does not show values: ``` ❯ hq server info --stats +----------------------+--+ | Stream connections | | | Stream registrations | | | Open files | |...

F-seq 1.85 craches out of memory error

4

F-seq 1.85 craches on one of my bed files (BAM ==> BED) with an out of memory error (F-Seq is allowed to use 240 GiB of memory) (the other 11...

It would be nice if fseq can convert the wig output files also to bed format. Now you need to run fseq 2 times to have the output in wig...

frawk is 3 times slower than mawk when reading/writing to piped commands opened by the awk process.

9

frawk is 3 times slower than mawk when reading/writing to piped commands opened by the awk process. Reading 2 input files from a pipe and writing to stdout: ```awk ❯...

Scientific notation is not supported in awk script.

2

Scientific notation is not supported in awk script, but works for parsing files with scientific notation. ```bash $ printf '6.18163e-27\n1.80782e-40\n2.38296e-05\n1.92843e-09\n7.37465e-39\n' | frawk '$1

If possible minimize clash between gawk and frawk flags

4

If possible minimize clash between gawk and frawk flags: ``` ❯ frawk -h frawk 0.4 Eli R. frawk is a pattern scanning and (semi-structured) text processing language USAGE: frawk [FLAGS]...

print does not print anything if not followed by a space or ";"

6

```bash $ echo 'test' | frawk '{print}' $ echo 'test' | frawk '{print }' test $ echo 'test' | frawk '{print;}' test $ echo 'test' | frawk '{print $0}' test...

Is it possilbe to build frawk with musl?

4

Is it possilbe to build frawk with musl? ```cargo +nightly build --release --target x86_64-unknown-linux-musl``` I always run in to problems with jemalloc. I just want to have a static version...