From 6877d917d43a15d88342684355fdf06ba0a62fed Mon Sep 17 00:00:00 2001 From: Shaun Jackman Date: Tue, 21 Jul 2009 20:44:20 +0000 Subject: [PATCH] 2009-07-21 Shaun Jackman * Release version 1.0.11. * Assemble colour-space reads. Read identifiers must be named with the suffixes F3 and R3. * Read files in qseq format. Thanks to Tony Raymond (tgr). * Prevent misassemblies mediated by tandem segmental duplications. A sequence XRRY, where R is a repeat sequence, could have been misassembled as XRY. (tgr) abyss-pe: * Integrate with Sun Grid Engine (SGE). A parallel, paired-end assembly can be run with a single qsub command. The parameters lib, np and k default to the qsub environment variables JOB_NAME (qsub -N), NSLOTS (qsub -pe) and SGE_TASK_ID (qsub -t) respectively. * The .pair file, the largest intermediate file, is now gzipped. ABYSS-P: * Bug fix. At k=19, k-mer would be distributed to even-numbered processes only. KAligner: * Multithreaded. The -j, --threads option specifies the number of threads to use. The order in which the alignments are output will vary from run to run, but the alignments are deterministic and will not vary. Each thread reads and aligns one file, so the reads must be in more than one file to use this feature. (tgr) git-svn-id: https://svn.bcgsc.ca/svn/abyss/trunk@49781 ad02020f-2a26-4133-947e-1829317c1416 --- ChangeLog | 29 +++++++++++++++++++++++++++++ configure.ac | 2 +- 2 files changed, 30 insertions(+), 1 deletion(-) diff --git a/ChangeLog b/ChangeLog index 64b8a5915..2c1ef9c6a 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,32 @@ +2009-07-21 Shaun Jackman + + * Release version 1.0.11. + * Assemble colour-space reads. Read identifiers must be named with + the suffixes F3 and R3. + * Read files in qseq format. Thanks to Tony Raymond (tgr). + * Prevent misassemblies mediated by tandem segmental duplications. + A sequence XRRY, where R is a repeat sequence, could have been + misassembled as XRY. (tgr) + + abyss-pe: + * Integrate with Sun Grid Engine (SGE). A parallel, paired-end + assembly can be run with a single qsub command. The parameters + lib, np and k default to the qsub environment variables JOB_NAME + (qsub -N), NSLOTS (qsub -pe) and SGE_TASK_ID (qsub -t) + respectively. + * The .pair file, the largest intermediate file, is now gzipped. + + ABYSS-P: + * Bug fix. At k=19, k-mer would be distributed to even-numbered + processes only. + + KAligner: + * Multithreaded. The -j, --threads option specifies the number of + threads to use. The order in which the alignments are output will + vary from run to run, but the alignments are deterministic and + will not vary. Each thread reads and aligns one file, so the reads + must be in more than one file to use this feature. (tgr) + 2009-06-18 Shaun Jackman * Release version 1.0.10. diff --git a/configure.ac b/configure.ac index 1e32ef60e..69c5ea847 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.59) -AC_INIT(abyss, 1.0.10, abyss@bcgsc.ca) +AC_INIT(abyss, 1.0.11, abyss@bcgsc.ca) AM_INIT_AUTOMAKE(foreign) AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp]) AC_CONFIG_HEADER([config.h])