release 2.1.4

Author: Ben Vandervalk

ChangeLog

@@ -1,3 +1,21 @@
+2018-11-09  Ben Vandervalk <benv@bcgsc.ca>
+
+	* Release version 2.1.4
+	* Major improvements to Bloom filter assembly contiguity and
+	correctness. Bloom filter assemblies now have equivalent scaffold
+	contiguity and better correctness than MPI assemblies of the same
+	data, while still requiring less than 1/10th of the memory. On
+	human, Bloom filter assembly times are still a few hours longer
+	than MPI assemblies (e.g. 17 hours vs. 13 hours, using 48
+	threads).
+
+	abyss-pe:
+	* Change default value of `m` from 50 => 0, which has the effect
+	of disallowing sequence overlaps < k-1 bp. QUAST tests on E. coli /
+	C. elegans / H. sapiens showed that both contiguity and
+	correctness were improved by allowing only overlaps of k-1 bp
+	between sequence ends.
+
 2018-11-05  Ben Vandervalk <benv@bcgsc.ca>
 
 	* Release version 2.1.3

Misc/samtobreak.hs

@@ -279,7 +279,7 @@ parseArgs = do
   where
   help = putStr (usageInfo usage options) >> exitSuccess
   tryHelp = "Try 'abyss-samtobreak --help' for more information."
-  version = "abyss-samtobreak (ABySS) 2.1.3\n"
+  version = "abyss-samtobreak (ABySS) 2.1.4\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

bin/abyss-pe

@@ -395,7 +395,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.1.3"
+	@echo "abyss-pe (ABySS) 2.1.4"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.1.3, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.1.4, abyss-users@bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 m4_include(m4/m4_ax_pthread.m4)
 AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects)
@@ -263,7 +263,7 @@ elif test x"$enable_werror" = x"yes"; then
 	AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
 else
 	# default
-	AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
+	AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra')
 fi
 
 # Build abyss-paired-dbg and abyss-paired-dbg-mpi

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.3" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.4" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.3" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.4" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.3" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.4" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br