Vamb 2.1

Release of Vamb 2.1

New features:

Support for PyTorch 1.2
Support for CUDA-accelerated clustering
Now writes lengths.npz, a vector of contig lengths to output directory.
Now checks BAM files' is not present, unsorted or sorted by readname
Now checks that the references in BAM file are same as references in FASTA file

Bugfixes:

Correctly compensate for float rounding error in cluster histogram function
Fixed bug where RPKM were consistently half their true value
Fixed a bug where all-zero rows could not be clustered
make_dataloader now no longer crashes when passed destroy=True
Fixed a NameError bug in vambtools.filterfasta that made it unusable
If specified more than 8 cores for bam file parsing, now actually uses more cores.
Fixed wrong error message if input contiglength npz array was not of integer type
Correctly print batchsteps in VAE training if they are None
Now raises a legible error if running Vamb on command line and length of RPKM and TNF does not match, even if refhashing is disabled.
Now also creates a rpkm.npz file if depths input is a JGI file.

Internal (interpreter-use) behaviour change

New function: vambtools.concatenate_fasta, which creates a concatenated sequence catalogue from multiple FASTA files, renames the sequences to conform to binsplitting, and makes sure the headers are unique.
New function: Added function parsebam.count_reads, that counts mapping read in BAM file
New function: parsebam.calc_rpkm that calculates RPKM from read counts and contig lengths
Removed function: Pearson correlation based clustering is no longer available
When labels is None, vamb.cluster.cluster now returns an interator of indices, not indices + 1
cluster.write_clusters now has a "rename" keyword. It will not rename clusters if set to False.
vambtools.loadfasta and vambtools.write_bins now has keywords "compress" and "compressed" (False by default), which causes sequences to be stored in compressed form.
parsebam.read_bamfiles now takes argument refhash, which shold be None or md5 hash that the references must hash to.
Argument minlength can now consistently be passed as None in functions of module parsebam, similar to the other filtering parameters.
benchmark.Contig is no longer immutable, and can now be desrialized using pickle.

Misc:

Improved validation of command line options
Now handles whitespace in FASTA sequences (tabs, and spaces only)
Increased numerical stability in RPKM estimation
Numerous documentation and performance improvements
Now warns user that VAE may overfit if less than 50,000 contigs are kept.
Output cluster names are now more legible and contains information about pre-binsplit cluster.