mSWEEP-v1.4.0 (10 March 2020)

[tmaklin]

mSWEEP-v1.4.0 (10 March 2020)

Beware the clichés of software naming edition.

New features

• Support parallel processing through the '-t' flags with excellent scaling in larger problems.
• Add possibility to match the input grouping indicators to the fasta file through the '--fasta' and '--groups-list' options.
• Add the '--bootstrap-count' option which allows resampling fewer input alignments than the original sample contains.
• Add possibility to specify the initial random seed for bootstrapping through the '--seed' option.
• Support reading in files compressed with bz2 or lzma if compiled on a machine that supports them.

Better error checking

• Validate that all input and output files exist and are accessible.
• Add possibility to validate the input grouping indicators when using Themisto pseudoalignments (resolves #4 ).
• Catch errors in several places that escaped in earlier versions.
• More informative error messages in the above-mentioned cases.

More efficient resource usage

• Parallel proceessing in the RCG optimization using OpenMP.
• Memory usage reduced by ~40% and in large problems.
• Single core performance increased by ~10% in large problems.

Better build pipeline

• Download dependencies when running cmake.
• Build without OpenMP if it is not supported.
• More aggressive compiler optimization flags.
• Support build and optimization with the Intel C compiler.

Internal changes

• Improve code structure and legibility.
• Use an external library (telescope) to read in pseeudoalignments from both kallisto or Themisto.
• Better internal storage for the pseudoalignments.
• Change the (rareish) reset step in the RCG optimization to be computationally more expensive but consume significantly less memory.
• Separate bootstrap and regular sample processing classes.