Matt Shirley

Hey @palao. I still need to take some time to digest this so thanks for your patience!

Thanks for the suggestion! I actually implemented `Faidx` using a memory-mapped file in very [early versions](https://github.com/mdshw5/pyfaidx/blob/4a598c8ca0b0dfa40031e61876ae387249978e07/pyfaidx/__init__.py), but didn't see much performance benefit. I think that you only avoid a system...

@Maarten-vd-Sande this is definitely *not* due to the Bio.bgzf implementation and is definitely due to my incomplete implementation of virtual offset calculations from the start of each contig. I started...

I've been meaning to take some time to write parsers for these binary files so that I can create QC visualizations of the positional and GC bias models and fragment...

Adding this work to [multiqc](https://github.com/ewels/MultiQC/blob/master/multiqc/modules/salmon/salmon.py) might be a natural starting point. I see there's also code to extract the FLD there right now, but have to admit I do not...

@mcsimenc I think the documentation is describing a binary representation of 32-bit unsigned integers that can be unpacked using the python [struct](https://docs.python.org/3/library/struct.html#examples) library. You'd need to know how many integers...

@mdshw5 Let me know if I can help out in any way. The idea of getting more metadata from salmon runs for QC purposes is definitely on my radar.

This seems like a fairly simple job for an external tool as well. What did you have in mind? Just transcript --> genomic coordinates in a table or are you...

@kikegoni this is something I started to work on but then quickly abandoned. I've uploaded the utility (`transcoorder`) that I started writing (https://github.com/mdshw5/transcoorder) for this purpose. If you find it...

The example output for SRR5024127 is: Transcript coordinate SAM: ``` s/docsource/analysis/SRR5024127/salmon/gencode_basic_exonic/mapped.bam | head -n10 @HD VN:1.0 SO:coordinate @SQ SN:ENST00000456328.2 LN:1657 DS:T @SQ SN:ENST00000450305.2 LN:632 DS:T @SQ SN:ENST00000488147.1 LN:1351 DS:T @SQ...