slow5tools-v1.3.0

What's Changed

• new ex-zd signal compression method. See the bioxiv preprint
• new subtool called degrade for lossy compression through bit elimination. Irreversible lossy compression, so be careful! See the bioxiv preprint
• new options to split subtool to enable demultiplexing a S/BLOW5 based on barcodes (or custom categories) from a tsv file (--demux, --demux-code, --demux-rid and --demux-uniq)
• documentation update (updates to faq, new datasets added to datasets and updates to commands) and workflows
• using $(MAKE) by @sashajenner in #126
• ./configure now supports --prefix (solves #124)

Many contributions by @sashajenner.

Full Changelog: v1.2.0...v1.3.0

slow5tools-v1.2.0

What's Changed

• big-endian support (request by #88) added - for all features except for svb-zd
• documentation improvement
• improve usability of slow5tools get (#113)

slow5tools-v1.1.0

changes/improvements

• minor s2f bug fix #96
• documentation improvements (more bash oneliners, faq, workflows, datasets, software etc)
• new --cite option added to slow5tools
• slow5tools skim can handle new fields (tracked_scaling_shift, tracked_scaling_scale, predicted_scaling_shift, predicted_scaling_scale, num_reads_since_mux_change, time_since_mux_change, num_minknow_events) that will be in S/BLOW5 files converted from POD5s
• slow5tools get has a new option --index option which can be used to specify a custom index location

slow5tools-v1.0.0

No changes from the previous version. Marking the fact that slow5tools is feature complete and stable.

slow5tools-v0.9.0

• many documentation improvements such as:
  • new examples workflows added to https://hasindu2008.github.io/slow5tools/workflows.html
  • new faq added to https://hasindu2008.github.io/slow5tools/faq.html
  • https://hasindu2008.github.io/slow5tools/software.html and https://hasindu2008.github.io/slow5tools/datasets.html added
• support for converting the latest FAST5 files
• updates to cmake (hiruna72) #87
• --skip option to slow5tools get: skip with a warning if a read is not found rather than erroring out (hiruna72) #86

slow5tools-v0.8.0

• slow5tools skim and cat are no longer experimental
• update slow5lib

slow5tools-v0.7.0

• New subtool called skim was added (still beta - use with caution and suggestions welcome)!

  Skims through requested components in a SLOW5/BLOW5 file. If no options are provided, all the SLOW5 records except the raw signal will be printed.
  Usage: slow5tools skim [OPTIONS] [SLOW5_FILE]
  
  OPTIONS:
      -t, --threads INT             number of threads [8]
      -K, --batchsize INT           number of records loaded to the memory at once [4096]
      --hdr                         print the header only
      --rid                         print the list of read ids only
      -h, --help                    display this message and exit
  
  

  Examples:

  # print all per-read metadata (except the raw signal)
  slow5tools skim file.blow5
  #print the list of read IDs
  slow5tools skim --rid file.blow5
  #print the SLOW5 header
  slow5tools skim --hdr file.blow5
  

• 3ff8bbb: improving search files log message in f2s (hiruna72)

• 4d8595c: include cases where certain field values can be zero(hiruna72)

slow5tools-v0.6.0

Changes are:

• now slow5tools can be built with HDF5 disabled, for those who just want to manipulate BLOW5 files (@lh3 thanks for the suggestion). To do so, call ./configure --disable-hdf5 && make or completely bypass the configure step and just call make disable_hdf5=1.
• usability improvements
• added new faqs and workflows

slow5tools-v0.5.1

• improvements to realtime f2s scripts (supports multiple processes now: -p option)
• fix for new Raw attribute in FAST5: num_minknow_events
• improvements to documentation

slow5tools-v0.5.0

• improved documentation and instructions for compilation on Apple Silicon
• updates and improvements to realtime-f2s that performs real-time FAST5 to BLOW5 conversion on the sequencer
• 6346341: use correct batch and thread numbers in slow5tools get command(hiruna72)
• dcb560e: slow5tools view fail if more than one input file is given (hiruna72)
• 2863ea2: fast indexing for zlib compressed BLOW5 files (~10X faster than before; see below; thanks @hiruna72 for the benchmark plot)