diff --git a/ChangeLog b/ChangeLog index 7a602bc18..422a8c8e6 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,51 @@ +2013-11-20 Anthony Raymond + + * Release version 1.3.7 + * Use long sequences to rescaffold scaffolds. May be run by + adding libraries to the `long’ parameter. When Scaffolding + with RNA-Seq contigs from a Trans-ABySS assembly, the genic + contiguity is greatly improved. + * Added support gcc 4.8+, and Mac OS X 10.9 Mavericks with clang. + * Licensed as GPL for non-commercial purposes. + + abyss-fac: + * Added e-size to contiguity statistics as described in the GAGE + paper. + + abyss-filtergraph: + * Bug fix. `--assemble’ will not fail an assertion. + * New option, --max-length, used to remove contigs over the + specified threshold. + * Trim 2-in 0-out tips when removing tips. + + abyss-map: + * Bug fix. Correctly set mapq=0 for reads that multi map. + + abyss-longseqdist: + * New program. Generate distance estimates between all contigs a + single read maps to. + + abyss-mergepairs: + * Report number of reads chastity filtered. + + abyss-overlap: + * Bug fix. Handle ambiguity codes. + + abyss-pe: + * Support BWA-MEM with assembly. Run using parameter + `aligner=bwamem’. + * Added another scaffolding stage using long sequences. May be + run by adding libraries to the `long’ parameter. + + ABYSS-P: + * Bug fix. Do not use awk to merge fasta files. + + abyss-samtobreak: + * Building bug fix. Check that ghc modules are installed. + + UnitTest: + * The Google C++ testing framework has been added to ABySS. + 2013-07-15 Anthony Raymond * Release version 1.3.6 diff --git a/bin/abyss-pe b/bin/abyss-pe index 4cad92569..b0e3d9bba 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -237,7 +237,7 @@ Report bugs to .\n' version: @printf '\ -abyss-pe (ABySS) 1.3.6\n\ +abyss-pe (ABySS) 1.3.7\n\ Written by Shaun Jackman.\n\ \n\ Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n' diff --git a/configure.ac b/configure.ac index 9162615dc..52f4b564b 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.59) -AC_INIT(ABySS, 1.3.6, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 1.3.7, abyss-users@bcgsc.ca, abyss, http://www.bcgsc.ca/platform/bioinfo/software/abyss) AM_INIT_AUTOMAKE(foreign subdir-objects) AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp]) diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index 228d9a596..b95277834 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2013-Jul" "ABYSS (ABySS) 1.3.6" "User Commands" +.TH ABYSS "1" "2013-Nov" "ABYSS (ABySS) 1.3.7" "User Commands" .SH NAME ABYSS \- assemble short reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1 index cf15e8a61..8117f2c71 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2013-Jul" "abyss-pe (ABySS) 1.3.6" "User Commands" +.TH abyss-pe "1" "2013-Nov" "abyss-pe (ABySS) 1.3.7" "User Commands" .SH NAME abyss-pe - assemble reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1 index 1a32b9e44..d03338ea5 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2013-Jul" "ABySS 1.3.6" "User Commands" +.TH abyss-tofastq "1" "2013-Nov" "ABySS 1.3.7" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br