perbase

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Add Forward/Reverse mapping counts

2

`samtools mpileup` reports forward and reverse mapping counts using uppercase letters (ATCGN) for F-mappings and lowercase (atcgn) for R. Indels have also separate symbols to specify if the event was...

25shmeckles

Support bedGraph output in only-depth

1

Support bedGraph output in only-depth: This is basically `perbase -z` output without header and chromosomes sorted by lexographically. This would allow to create bigwig files relatively easily. (naive sorting takes...

ghuls

In release mode doe a profile guided optimization pass like hck https://github.com/sstadick/hck/blob/master/pgo.sh This improves performance ~5-30%

sstadick

Look into writing my own pileup engine

2

It would be nice to have Send / Sync built in all the way down.

sstadick

This needs to be done in order to validate the "fast" term. I may way to do this till `in-depth` tool has also been added to benchmark all at the...

sstadick

For example if a bedfile is missing you get this: ``` thread '' panicked at 'Parsed BED to intervals: No such file or directory (os error 2)', /opt/conda/conda-bld/perbase_1602523225266/work/src/lib/par_granges.rs:131:66 ``` Which...

sstadick

Output more metrics in line with `bam-readcount`, but better formatted.

sstadick

Add support of readgroup awareness and filtering

1

see sambamba depth

sstadick

Missing bam/cram file should return an error code

2

Hi, when running perbase base-depth with an incorrect BAM/CRAM path, even though stderr reports `thread '' panicked at 'Indexed BAM/CRAM: FileNotFound [...] perbase/src/lib/par_granges.rs:159:72`, it seems that no error code was...

patbohn

not all region return when using a bed file

1

Hi, I am using the perbase base-depth using a bed file as site list and --keep-zeros to get info for all my regions described in the bed file, however, the...

FunGeST