SortByName

Script: sortbyname.sh (alias for bbsort.sh) Package: jgi Class: sort.SortByName

This is an alias script that redirects to bbsort.sh using pushd/popd directory resolution and BASH_SOURCE[0] symlink handling. It provides identical functionality to bbsort.sh for backwards compatibility.

Automatic Redirect

The sortbyname.sh script is a simple wrapper that calls bbsort.sh with all the same parameters.

You will be automatically redirected to the complete BBSORT documentation in 3 seconds.

If you are not redirected automatically: Click here to go to BBSORT documentation

About This Tool

The bbsort tool (accessible via both bbsort.sh and sortbyname.sh) sorts sequencing reads using the sort.SortByName class with multiple concurrent processing strategies:

Name-based sorting: Uses ConcurrentReadInputStream and ConcurrentReadOutputStream to sort reads alphabetically by name with efficient comparison operations
Sequence sorting: Implements sequence-based sorting via Read.sequence comparison with optional reverse complementation for genomic analysis
Quality-based sorting: Evaluates quality scores using Read.quality arrays with statistical aggregation and optional trimming integration
Length-based sorting: Uses Read.length() method with numeric comparison for read length distribution analysis and filtering
Custom field sorting: Supports header-based field extraction and sorting with configurable delimiters using Read.id parsing and split() operations

Memory Management: Utilizes ListNum<Read> collections with concurrent processing, efficient in-memory sorting algorithms, and optional external sort for large datasets exceeding available RAM.

For complete parameter documentation and examples, see the full BBSORT documentation.

Basic Usage

# Both commands work identically via sort.SortByName:
sortbyname.sh in=reads.fq out=sorted.fq
bbsort.sh in=reads.fq out=sorted.fq

# Advanced sorting modes supported:
sortbyname.sh in=reads.fq out=sorted.fq sort=sequence
sortbyname.sh in=reads.fq out=sorted.fq sort=length reverse=t
sortbyname.sh in=reads.fq out=sorted.fq sort=quality ascending=f

Processing Architecture: Both scripts invoke java -cp bbmap.jar sort.SortByName with 4-buffer concurrent I/O streams, automatic format detection via FileFormat.testInput(), and configurable compression levels through ReadWrite.setZipThreads().

Support

For questions and support:

Email: bbushnell@lbl.gov
Documentation: bbmap.org