This is the v1.3 release of khmer featuring a new FAST[AQ] parser from the SeqAn project.
Docs at: https://khmer.readthedocs.org/en/v1.3/
Fixes the two multithreaded reading of sequence files issues: FASTQ parsing and the recently found read dropping issue. Several khmer scripts now support reading from non-seekable plain and gziped FAST[AQ] files (a.k.a pipe or streaming support). @mr-c #642
restore threading to load-graph.py #699 @mr-c
increase filter_abund.py coverage #568 @wrightmhw Provide scripts/ testing coverage for check_space_for_hashtable #386 #678 #718 @b-wyss Use absolute URI in CODE_OF_CONDUCT #684 @jsspencer give SeqAn credit #712 @mr-c Added testing to make sure all sandbox scripts are import-able and execfile-able. #709 @ctb reduce memory requirements to run tests #701 @ctb Two minor bug fixes to sandbox scripts #706 @ctb Upgrade of trim-low-abund for better, more profitable streaming. #601 @ctb Add --force or --expert or --ignore flag to all khmer scripts that do sanity checking #399 #647 @jessicamizzi Add XDECREF for returned read tuple in ReadParser.read_pair_iterator() #693 @mr-c @camillescott
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 #266
If your k-mer table is truncated on write, an error may not be reported; this is being tracked in https://github.com/dib-lab/khmer/issues/443. 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 #23
Some scripts only output FASTA even if given a FASTQ file. This issue is being tracked in #46
A user reported that abundance-dist-single.py fails with small files and many threads. This issue is being tracked in #75
@mr-c, @ctb, @camillescott, @b-wyss, @wrightmhw, @jsspencer