khmer v1.1 release notes

This is v1.1, a minor version release; this version adds several new scripts.

Docs at:

Release notes w/links:

New items of note:

  • removed unnecessary files from PyPI package; distribution is now under 2 MB (#419) @mr-c
  • tests are now distributed with package and can be run after 'pip install' (#451) @mr-c
  • complain properly on file read failures (#333) @ctb
  • Sequence loading scripts will now report total numbers of k-mers if given --report_total_kmers (#491/#429) @mr-c
  • added metagenome protocol to acceptance testing (#472) @SherineAwad @ctb

Notable bugs fixed/issues closed:

  • removed sandbox/ (superseded by scripts/ --no-tagset) (#480, @wrightmhw)
  • promoted to scripts (#461, @wrightmhw)
  • promoted to scripts (#436, @wrightmhw)
  • remove incorrect filesystem space check from (#452, @chuckpr)
  • when counting hash writes fail, produce error message (#411, @znruss)
  • removed a number of memory leaks found by Coverity and valgrind (#451, @mr-c)
  • updated reservoir sampling to produce multiple subsamples with -S (#197, @ctb)
  • fixed pip2, python2 issues (#428 and #485, @accaldwell @mr-c)
  • removed untested/unused code and scripts (#438, @mr-c)

Known issues:

All of these are pre-existing.

Some users have reported that will utilize more memory than it was configured for. This is being investigated in

Some FASTQ files confuse our parser when running with more than one thread. For example, while using If you experience this then add "--threads=1" to your command line. This issue is being tracked in

If your k-mer table is truncated on write, an error may not be reported; this is being tracked in However, khmer will now (correctly) fail when trying to read a truncated file (See #333).

Paired-end reads from Casava 1.8 currently require renaming for use in normalize-by-median and abund-filter when used in paired mode. The integration of a fix for this is being tracked in

Some scripts only output FASTA even if given a FASTQ file. This issue is being tracked in

A user reported that fails with small files and many threads. This issue is being tracked in


@mr-c, @ctb, @camillescott, @wrightmhw, @chuckpr, @luizirber, @accaldwell, @znruss

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