From 9ee0ad3b49eec425c5a45f0d96e6e67895596ff7 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 8 Jan 2015 15:10:38 -0500 Subject: [PATCH] add release notes --- doc/release-notes/release-1.3.md | 57 ++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 doc/release-notes/release-1.3.md diff --git a/doc/release-notes/release-1.3.md b/doc/release-notes/release-1.3.md new file mode 100644 index 0000000000..b55bf31528 --- /dev/null +++ b/doc/release-notes/release-1.3.md @@ -0,0 +1,57 @@ +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/ + +## New items of note: + +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 + +## Notable bugs fixed/issues closed: + +restore threading to load-graph.py #699 @mr-c + +## Additional fixes/features + +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 + +## Known issues: + +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/ged-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 + +## Contributors + +@mr-c, @ctb, @camillescott, @b-wyss, @wrightmhw, @jsspencer