f5c-v0.7

Major changes from f5c-v0.6 are:

• the event alignment tsv output now prints the strand column to be compatible with nanopolish output (#86) (--meth-out-version can be set to 1 if the previous format is preferred)
• slow5 support [--slow5 option for f5c index, call-methylation and eventalign, more info here]
• -w option can now also take a bed file containing a list of regions (#84)
• minor bug fixes (bugs that affected -w option (#90) and sequencing summary files (#85)
• better support for fast5 with vbz compression (a script that attempts to automatically install vbz on Linux x86 or aarch64. More info here)

f5c-v0.6

Major changes from f5c-v0.5 are:

• Implementation of --samples and --signal-index for eventalign module [#74]
• Major performance optimisation to eventalign when running at a higher number of threads (fixes a bottleneck when writing the output)
• Custom nucleotide or methylation models are fully supported now (--kmer-model and --meth-model) and the k-mer size can now be 5 or 6
• Supports RNA event alignment (eventalign with --rna option) [#73] (thanks @a-slide for the suggestion and testing)
• Minor bug fixes
• Major code cleanup and refactoring

f5c-v0.5

Major changes from f5c-0.4 are:

• multi-process indexing (>10x faster f5c index with --iop and -t options)

• preset parameter profile (-x option)

• updated manpage

• added pipeline scripts for HPC environment

• skip over-segmented read to avoid memory overflow crashes

• source code restructuring

• better error/help messages

• option --meth-model

• freq-merge is improved

• bugfixes (mainly a bug that affected chromosome names containing ':' in meth-freq)

f5c-v0.4

Major changes from f5c-0.3 are:

• fixed a bug that affected cuda-dev-id (#57)
• implemented -w option to allow a specific genomic interval (#58)
• implemented --summary, --sam, --scale-events, --print-read-names options for eventalign
• implemented --meth-out-version to print strand information in methylation calling output (#60)
• new subtool freq-merge for merge meth-freq outputs (by @hiruna72)
• --profile (-x) option to set device profiles (by @dkhyland)
• fixed compiler warnings for MacOS
• changed --min-mapq to 20 by default (which was 30 previously)

f5c-v0.3-beta

• full multifast5 support (taken from Nanopolish)
• multi-process based I/O model for fast5 access (to circumvent I/O bottleneck due to limitation in multi-threaded HDF5 library)
• some bug fixes (mainly a memory allocation bug that affected 32 bit systems)

f5c-v0.2-beta

• minor bug fixes
• improvements to the CPU-GPU resource utilisation advisor
• a new meth-freq module added, mostly by @lamcw
  to calculate methylation frequency at genomic CpG sites (optimised nanopolish calculate_methylation_frequency.py)
• a new eventalign module added, mostly by @hiruna72
  to align nanopore events to reference k-mers (optimised nanopolish eventalign)

f5c-v0.1-beta

version 0.1-beta

f5c-v0.0-alpha

initial alpha release for testing