Brian Bushnell

-s flag is unclear

2

It's not obvious what the -s flag does. There are basically 4 use cases for a program that does a transform on some data: 1) program infile outfile 2) program...

DSRC nonfunctional in Windows

2

I'm running Windows 7 64-bit. I can execute dsrc with no arguments, and it prints usage information. But if I tell it to do something, it crashes: C:\temp\ecoli>dsrc c readx.fq...

Add BBTools Java implementation for fqcnt benchmark

1

This PR adds BBTools FastqScan as a Java implementation for the fqcnt benchmark. ## Implementation Details - Uses BBTools' FastqScan tool with multithreaded SIMD-accelerated parsing - Wrapper script: `fqcnt_java_bbtools.sh` -...