582 changed files with 40,527 additions and 31,772 deletions.
The team has been hard at work since v0.8 to refine the codebase into a stable product.
https://khmer.readthedocs.org/en/latest/
With the 1.0 release we are making a commitment to using Semantic Versioning[0]: the version number will reflect the impact of the changes between releases. New major versions will likely require you to change how you use the project. Minor versions indicate new functionality that doesn't impact the existing. Patch versions indicate backwards-compatible fixes. Right now we are limiting this promise to the command-line interface. A future release will introduce a stable and mature Python API to the khmer project and at that time we will extend the version system to include that API.
CITATION: Each script now outputs information on how to cite it. There is a new paper to describes the project overall: MR Crusoe et al., 2014. doi: 10.6084/m9.figshare.979190
The documentation for the scripts has undergone an overhaul. The scripts now output extensive notes and the formal documentation website is generated from the scripts themselves and will never be out of sync.
git clone of the khmer repo reqs > 0.5 GiB #223 @mr-c new khmer/file module #357 @RamRS Floating point exception in count-overlap.py #282 @qingpeng add documentation for sample-reads-randomly #192 @mr-c only build zlib and bzip2 when needed #168 @mr-c
khmer tools should output intelligent error messages when fed empty files #135 @RamRS set IParser::ParserState::ParserState:fill_id to zero at initialization #356 @mr-c demote nose & sphinx to extra dependencies. #351 @mr-c CID 1054792 (Medium) Uninitialized scalar field (UNINIT_CTOR) #179 @mr-c CID 1077117 (Medium): Division or modulo by zero (DIVIDE_BY_ZERO) #182 @mr-c if --savehash is specified then don't continue if there is not enough free disk space #245 @RamRS finish fixing implicit downcasts #330 @mr-c Clean up compile warnings in subset.cc #172 @mr-c all scripts need to output their version #236 @mr-c environmental variables need documenting #303 @mr-c C++ code should be consistently formatted #261 @mr-c Clean up ancillary files #146 @mr-c squash option not implemented in abundance-dist-single.py #271 @RamRS Add documentation on how to tie into a particular tagged version #29 @mr-c pip install -e fails with compile error #352 @mr-c remove the unused KTable object #337 @luizirber zlib 1.2.3 -> zlib 1.2.8 #336 @mr-c CID 1173035: Uninitialized scalar field (UNINIT_CTOR) #311 @mr-c CID 1153101: Resource leak in object (CTOR_DTOR_LEAK) #309 @mr-c remove khmer::read_parsers::IParser::ParserState::thread_id #323 @mr-c several modifications about count-overlap.py script #324 @qingpeng fixed runscript to handle SystemExit #332 @ctb CID 1063852: Uninitialized scalar field (UNINIT_CTOR) #313 @mr-c [infrastructure] update to new Doxyfile format, make version number autoupdate #315 @mr-c Removed an extraneous using namespace khmer; in kmer.hh, #276 @fishjord Minimum and recommended python version #94 @mr-c KmerCount class appears to be unused #302 @mr-c If loadhash is specified in e.g. normalize-by-median, don't complain about default hashsize parameters #117 @RamRS
All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more memory than it was configured for. This is being investigated in https://github.com/dib-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one thread. For example, while using load-into-counting.py. If you experience this then add "--threads=1" to your command line. This issue is being tracked in https://github.com/dib-lab/khmer/issues/249
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 https://github.com/dib-lab/khmer/issues/247 and https://github.com/dib-lab/khmer/issues/96 and https://github.com/dib-lab/khmer/issues/246
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 https://github.com/dib-lab/khmer/issues/23
annotate-partitions.py only outputs FASTA even if given a FASTQ file. This issue is being tracked in https://github.com/dib-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and many threads. This issue is being tracked in https://github.com/dib-lab/khmer/issues/75