khmer v1.0.1 release notes

This is bugfix release. Note: the installation instructions have been slightly simplified.

New items of note:

This release successfully installs and passes its unit tests on Debian 6.0 "Squeeze", Debian 7.0 "Wheezy", Fedora 19, OS X 7 "Lion", OS X 8 "Mountain Lion", Red Hat Enterprise Linux 6, Scientific Linux 6, Ubuntu 10.04 LTS, and Ubuntu 12.04 LTS. Thanks to the UW-Madison Build and Test Lab for their testing infrastructure.

Notable bugs fixed/issues closed:

fixed thread hanging issue #406 @ctb Explicit python2 invocation #404 @mr-c, fix to correct zlib packaging #365 @mr-c fixed check_space_for_hashtable to use args.n_tables #382 @ctb Bug fix: error on missing .ht input file, actual input file is .pt #391 @mr-c

Minor updates

include in v1.0.1 #409 @ctb updated normalize-by-median documentation for loadtable #378 @ctb updated diginorm for new FP rate info; corrected spelling error #398 @ctb Add spellcheck to code review checklist. #397 @ctb

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 (hashfile) gets truncated, perhaps from a full filesystem, then our tools currently will get stuck. This is being tracked in and

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 only outputs 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, @luizirber, @RamRS, @ctSkennerton

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