2009-07-21 Shaun Jackman <[email protected]>

    * 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

@@ -1,3 +1,32 @@
+2009-07-21  Shaun Jackman  <[email protected]>
+
+	* 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  <[email protected]>
 
 	* Release version 1.0.10.

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.59)
-AC_INIT(abyss, 1.0.10, [email protected])
+AC_INIT(abyss, 1.0.11, [email protected])
 AM_INIT_AUTOMAKE(foreign)
 AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp])
 AC_CONFIG_HEADER([config.h])