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2014-07-09 Anthony Raymond <[email protected]> | ||
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* Release version 1.5.2 | ||
* First official release of Konnector and abyss-bloom. | ||
* More GCC 4.8+ fixes! Modified Boost install instructions. | ||
* Fixed rare bug when parsing output of BWA. | ||
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ABYSS: | ||
* New option, --mask-cov, use kmers with lowercased bases, but | ||
don't count them towards multiplicity. | ||
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abyss-bloom: | ||
* Construct reusable Bloom filter files for use with Konnector. | ||
* Perform boolean operations on two or more bloom filters. | ||
Currently supports union and intersection operations. | ||
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abyss-fixmate: | ||
* Check for boost 1.43+ when using `unordered_map::quick_erase`. | ||
* New option, --all, to report all alignments. | ||
* Set mate unmapped flag for mateless reads. | ||
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abyss-longseqdist: | ||
* Fixed `error: invalid CIGAR` when reading BWA output. | ||
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configure: | ||
* Include mpi and boost libraries as system libraries. Silences | ||
warnings (treated as errors) when compiling with GCC 4.8+. | ||
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konnector: | ||
* Merge read pairs into a single sequence (pseudoread) by | ||
building a Bloom filter de Bruijn graph and searching for paths | ||
between the paired end reads. Input reads may be | ||
FASTA/FASTQ/SAM/BAM. The input files must be sorted by read name | ||
and may not contain orphan reads. | ||
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2014-05-07 Anthony Raymond <[email protected]> | ||
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* Release version 1.5.1 | ||
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@@ -24,7 +59,7 @@ | |
* Portability fixes for Fujitsu C Compiler. | ||
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abyss-pe: | ||
* New parameter, `Q`, to mask low quality bases to N. | ||
* New parameter, `Q`, to mask low quality bases to N. | ||
* New parameter, `xtip=1`, to remove 2-in 0-out tips. | ||
* New parameter, `ss=1`, to perform strand-specific assembly | ||
using ssRNA-Seq libraries. | ||
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@@ -125,7 +160,7 @@ | |
* Improved documentation for GitHub devs. | ||
* ABYSS-P performance improvement. | ||
* Various portability and bug fixes. | ||
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abyss-mergepairs: | ||
* Fix program name. | ||
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@@ -168,7 +203,7 @@ | |
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abyss-pe: | ||
* Attempt to fill scaffold gap with consensus of all paths between | ||
contigs. | ||
contigs. | ||
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AdjList: | ||
* Increase the default value of m from 30 to 50. | ||
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@@ -263,7 +263,7 @@ Report bugs to <[email protected]>.\n' | |
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version: | ||
@printf '\ | ||
abyss-pe (ABySS) 1.5.1\n\ | ||
abyss-pe (ABySS) 1.5.2\n\ | ||
Written by Shaun Jackman and Anthony Raymond.\n\ | ||
\n\ | ||
Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n' | ||
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AC_PREREQ(2.62) | ||
AC_INIT(ABySS, 1.5.1, [email protected], abyss, | ||
AC_INIT(ABySS, 1.5.2, [email protected], abyss, | ||
http://www.bcgsc.ca/platform/bioinfo/software/abyss) | ||
AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects) | ||
AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp]) | ||
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