2013-07-15  Anthony Raymond  <traymond@bcgsc.ca>

	* Release version 1.3.6
	* Improved documentation for GitHub devs.
	* ABYSS-P performance improvement.
	* Various portability and bug fixes.
	
	abyss-mergepairs:
	* Fix program name.

	abyss-fac:
	* New option --exp-size to give the expected genome size needed
	for NG50 calculation.
	* New option --count-ambig include ambiguities in calculations.

	ABYSS/ABYSS-P:
	* Performance improvement. Runtime reduced by ~20%.
	* Fix support for MPICH.

	abyss-map:
	* No longer require POPCNT instruction.
	* New option --order to force output order the same as input.

	abyss-filtergraph:
	* New option --remove to remove specified contigs from graph.

	PopBubbles:
	* Bug fix. Setting branches > 2 will now work.

	abyss-fixmate:
	* Improved error when first and second read IDs do not match.
	* New option --cov to compute and store the physical coverage in
	a Wiggle file.

	AdjIO:
	* Bug fix for non-GCC compilers.

2013-03-04  Anthony Raymond  <traymond@bcgsc.ca>

	* Release version 1.3.5
	* Standardized --help message format.
	* Improve documentation.
	* Merge overlapping read pairs.
	* Layout and merge contigs using sequence overlap graph.
	* Attempt to fill scaffold gap with consensus of all paths between
	contigs.

	abyss-pe:
	* Attempt to fill scaffold gap with consensus of all paths between
	contigs. 

	AdjList:
	* Increase the default value of m from 30 to 50.

	abyss-overlap:
	* Increase the default value of m from 30 to 50.
	* New options, --tred and --no-tred. Remove transitive edges.
	Default --tred.

	abyss-mergepairs:
	* New program. Merges overlapping read pairs.

	ABYSS-P:
	* Bug fix. Exit when there is a problem reading a file.
	* Don't store sequences in the rank 0 process when using at least
	1000 cores. Improves memory distribution with large number of
	cores.

	abyss-fac:
	* Increase the default value of t from 200 to 500.

	DistanceEst:
	* Bug fix. Exit with success if there is only one contig. Fixes
	this error:
	DistanceEst: DistanceEst.cpp:534: int main(int, char**): Assertion `in' failed.
	* Bug fix. Fix the bug causing this error:
	DistanceEst: error: The observed fragment of size 128 bp is shorter than 2*l (l=71). Decrease l to 64.
	* Bug fix. Correctly estimate distance using MLE when l=0.

	abyss-layout:
	* New program. Layout contigs using the sequence overlap graph.

	abyss-map:
	* Return helpful error when query ID starts with '@`
	* New options, --chastity and --no-chastity. Ignore chastity
	failed reads. Default --no-chastity.

	abyss-samtobreak:
	* New script. Calculate contig and scaffold contiguity and
	correctness metrics.

	abyss-fixmate:
	* New option, l. Minimum alignment length. Set unmapped flag if
	the CIGAR match length is too small.
	* Print all alignments when the histogram output file not given.
	* Print SAM header to the same file when given.

2012-05-30  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.3.4.
	* Do not extend paths, which can cause misassemblies.
	* Increase the default value of m from 30 to 50.
	* Various portability fixes.

	abyss-pe:
	* Increase the default value of m from 30 to 50 to reduce the
	likelihood of misassemblies.
	* Integrate with SLURM. Thanks to Timothy Carlson.

	ABYSS:
	* Use CityHash64 rather than Bob Jenkins' hashlittle.

	SimpleGraph:
	* Do not extend paths. Closes #8. Extending paths can cause
	misassemblies when the de Bruijn graph is incomplete.

	MergePaths:
	* Bug fix. Closes #6. Fix the bug causing the error:
	Assertion `!m_ambig' failed.

	abyss-fatoagp:
	* New script. Create a FASTA file of scaftigs and an AGP file.

2012-03-13  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.3.3.
	* New parameter, l. Specify the minimum alignment length when
	aligning the reads to the contigs.
	* Improve the scaffolding algorithm that identifies repeats.
	* Improve the documentation.

	abyss-pe:
	* New parameter, l. Specify the minimum alignment length when
	aligning the reads to the contigs. This option may be specified
	per library. The default value is k.
	* New parameter, S. Specify the minimum contig size required for
	building scaffolds.
	* New parameter, N. Specify the minimum number of pairs required
	for building scaffolds.
	* Integrate with Load Sharing Facility (LSF).
	* Calculate the assembly contiguity statistics.

	KAligner, abyss-map:
	* Rename the minimum alignment length option -k to -l.

	DistanceEst:
	* Dual licensed under the GPL and BCCA-Academic licenses.
	* New options, --fr and --rf. Specify the orientation of the
	library. The default behaviour is to detect the orientation.
	* New options, --mind and --maxd. Specify the minimum and maximum
	distances for the maximum likelihood estimator.
	* New option, -l, --min-align. Specify the minimum alignment
	length of the aligner, which can improve distance estimates.
	* Increase the default minimum mapping quality, -q, to 10, was 1.

	MergePaths:
	* Bug fix. Fix the bug causing the error:
	Assertion `count(it2+1, path2.end(), pivot) == 0' failed.

	PathConsensus:
	* Bug fix. Fix the bug causing the error:
	Assertion `fstSol.size() == sndSol.size()' failed.

	MergeContigs:
	* Calculate the assembly contiguity statistics.

	abyss-scaffold:
	* Improve the algorithm that identifies repeats.
	* Remove simple cycles from the scaffold graph.
	* Calculate the assembly contiguity statistics.
	* The option -s may specify a range, such as -s200-10000,
	to find the value of s that maximizes the scaffold N50.

	abyss-fac:
	* New option, -m, --mmd. Output MultiMarkdown format.

	abyss-index:
	* New option, -a, --alphabet. Specify the alphabet.
	* New option, --bwt. Output the Burrows-Wheeler transform.

	abyss-samtoafg:
	* New script. Convert a SAM file to an AMOS AFG file.

	README, README.html, abyss-pe.1:
	* Improve the documentation.

2011-12-13  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.3.2.
	* Enable scaffolding by default.
	* Remove small shim contigs.
	* Improved distance estimates.
	* Reduce sequence duplication.
	* Read compressed files on Mac OS X.

	abyss-pe:
	* Enable scaffolding by default. If the mp parameter is not
	specified, use a default value of ${pe} or ${lib}.
	* Support using bowtie2 to align reads to contigs by specifying
	aligner=bowtie2.
	* The default aligner is abyss-map.
	* Output the scaffold overlap graph, ${name}-scaffolds.dot.
	* Set DYLD_FORCE_FLAT_NAMESPACE to read compressed files on OS X.

	ABYSS:
	* Can read k-mer count data from a Jellyfish file with extension
	.jf for k-mer counts or .jfq for q-mer counts. Jellyfish must be
	installed.
	* Bug fix. Fix the bug causing the error
	bool chomp(std::string&, char): Assertion `s.length() > 1' failed.

	abyss-filtergraph:
	* New program. Remove small shim contigs that add no useful
	sequence to the assembly. Thanks to Tony Raymond (tgr).

	PopBubbles:
	* New option, -a, --branches. Specify the maximum number of
	branches of a bubble that may be popped. Default is 2.
	* Use DIALIGN-TX for multiple sequence alignment. Thanks to tgr.

	DistanceEst:
	* Improved distance estimates.

	abyss-joindist:
	* Remove this program. Use abyss-todot instead.

	MergePaths:
	* Use a non-greedy algorithm that reduces sequence duplication but
	may reduce contiguity. The greedy algorithm may be used by
	specifying the option --greedy.

	abyss-fixmate:
	* Do not output query names by default.

	configure:
	* New option, --enable-samseqqual. Enable SAM sequence and quality
	fields.

2011-10-24  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.3.1.
	* Read sequence files in SRA format. The tool fastq-dump from the
	sratoolkit must be installed.
	* Read a contig overlap graph in the ASQG format of SGA.
	* Fix compile errors for Mac OS X.
	* Fix the bug that caused the line number of an error in a FASTQ
	file to be reported incorrectly.

	abyss-pe:
	* Support using BWA-SW to align reads to contigs by specifying
	aligner=bwasw.
	* The parameter ALIGNER_OPTIONS may be used to specify a different
	value for k when aligning using abyss-map.
	* New target, bam, may be used to produce a final BAM file of the
	reads aligned to the scaffolds.

	KAligner:
	* Fix the bug causing the error:
	Assertion `qstep >= 0 && qstep <= m_hashSize' failed.

	abyss-scaffold:
	* The result is independent of the order in which the mate-pair
	libraries are specified.
	* Permit scaffolding contigs that have non-numeric identifiers.
	* The overlap graph is optional.

	abyss-todot:
	* Convert adj, dist or ASQG formatted graph files to dot format.
	* Merge multiple graph files into one.

2011-09-09  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.3.0.
	* Use mate-pair libraries to scaffold contigs.
	* Support CASAVA-formatted FASTQ files.
	* Bug fix. Do not trim quality 41 bases from the ends of reads.
	* Boost C++ Libraries are required to compile ABySS.

	abyss-pe:
	* New parameter, mp, to specify the mate-pair libraries to be used
	for scaffolding.
	* Increase the default value for s from 100 to 200.
	* Set the default value for n to 10.
	* Integrate with PBS.

	abyss-scaffold:
	* New program. Scaffold using mate-pair libraries.

	DistanceEst:
	* Ignore multimapped alignments with a mapping quality of zero.
	* New option, -q, --min-mapq. Ignore alignments with mapping
	quality less than this threshold. Default is 1.
	* Do not use OpenMP 3.0.

	PopBubbles:
	* Scaffold over complex bubbles with the option --scaffold.
	Disabled by default.

	MergePaths:
	* Fix a bug that causes PathOverlap to die with the error:
	Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
	Assertion `e.second' failed.
	* New option, --no-greedy. Use a non-greedy algorithm that reduces
	sequence duplication but reduces contiguity. Disabled by default.

	KAligner:
	* Performance improvements. Thanks to Tony Raymond (tgr).
	* The output is printed in the same order as the input when
	multithreaded. (tgr)

	abyss-map:
	* New program. Use the BWT and FM-index to find the longest common
	substring. To use it, specify the option aligner=map to abyss-pe.

	abyss-index:
	* New program. Build a FM-index of a FASTA file.

	abyss-bowtie:
	* Use abyss-tofastq --interleave to speed up abyss-fixmate.

	abyss-bwa:
	* Use bwa index -a bwtsw by default.
	* Use abyss-tofastq --interleave to speed up abyss-fixmate.

	abyss-fac:
	* Report N80, N50 and N20. Do not report median and mean.
	* Increase the default minimum contig size threshold, option -t,
	from 100 to 200.

	abyss-fixmate:
	* Set the mapping quality of both alignments to the minimum
	mapping quality of the pair of alignments.

	abyss-tofastq:
	* New option, -i, --interleave. Interleave the files.

	configure:
	* New option, --with-boost. Specify the path for Boost.
	* New option, --disable-popcnt. Do not use the popcnt instruction.

2011-04-15  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.7.

	abyss-pe:
	* Support using bwa or bowtie to align reads to contigs.
	Specify aligner=bwa or aligner=bowtie.
	* Integrate with IBM LoadLeveler.

	PopBubbles:
	* Use an affine gap penalty.
	* The default maximum bubble length is 10 kbp.
	* New option, --scaffold. Scaffold over bubbles with insufficient
	sequence identity to be popped.

	SimpleGraph:
	* New parameter d to specify the acceptable error of a distance
	estimate. The default is 6 bp.

	PathConsensus:
	* Use an affine gap penalty.

	MergePaths:
	* Fix a bug that causes PathOverlap to die with the error:
	Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
	Assertion `e.second' failed.

2011-02-07  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.6.
	* Find contigs that overlap by fewer than k-1 bp.
	* Pop bubbles with sufficient sequence identity.
	* Merge paths that overlap unambiguously.

	abyss-pe:
	* New parameter, m, the minimum number of overlapping bases.
	The default is 30.
	* The minimum sequence identity parameter, p, applies to both
	PopBubbles and PathConsensus.

	ABYSS:
	* Support values of k larger than 96. The maximum value of k is
	set when compiling using `configure --enable-maxk´.

	AdjList:
	* Find sequences that overlap by fewer than k-1 bp. The parameter
	m specifies the minimum number of overlapping bases.

	PopBubbles:
	* Align both branches of the bubble and pop bubbles whose sequence
	identity is sufficient, at least 90% by default.
	* New parameter, p, the minimum identity required.
	* The maximum bubble size is unlimited by default. This limit can
	be changed using the parameter b.

	SimpleGraph:
	* Extend each path as long as is unambiguously possible.

	PathOverlap:
	* Merge paths that overlap unambiguously.

	MergeContigs:
	* Perform an alignment of the two sequences when no simple overlap
	is found.

	abyss-fac:
	* New option, -g. Specify the expected genome size.

2010-11-15  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.5.

	AdjList:
	* Fix the colour-space-specific bug causing the error
	Assertion `seq.length() > (unsigned)opt::overlap' failed.

	PathConsensus:
	* Fix the bug causing the error
	Assertion `fstSol.size() == 1' failed.

	abyss-fixmate:
	* Do not output the @RG header record at the end of the output
	that gives the median fragment size. It breaks `samtools view -S`.
	* --no-qname: New option. Set the qname to *.

2010-10-13  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.4.

	ABYSS-P:
	* Fix the bug causing the error
	Unexpected sequence extension message.

	KAligner:
	* Reduce the amount of memory used by KAligner.

	PathConsensus:
	* New program. Replace gaps of Ns that span a region of ambiguous
	sequence with a consensus sequence of the possible sequences that
	fill the gap. By default a minimum 90% identity is required. This
	default can be changed with the parameter, p. The consensus
	sequence uses IUPAC-IUB ambiguity codes. DIALIGN-TX is used for
	the multiple sequence alignment.

	PathOverlap:
	* Fix the bug causing the error
	Assertion `back(paths, u) == front(paths, v)' failed.

2010-09-08  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.3.

	ABYSS-P:
	* Bug fix. Fix the bug causing the error
	Assertion `m_comm.receiveEmpty()' failed.

	PopBubbles:
	* Bug fix. Fix the bug causing the error
	error: unexpected ID

	PathOverlap:
	* Include the single-end contigs in the overlap graph.

	abyss-pe:
	* Output an overlap graph of the paired-end assembly in the file
	${name}-contigs.dot.
	* Do not create the intermediate file ${name}-4.fa.

	abyss-adjtodot:
	* Convert an overlap graph in adj format to Graphviz dot format or
	SAM alignment format.

2010-08-25  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.2.
	* Merge contigs after popping bubbles.
	* Handle multi-line FASTA sequences.
	* Report the amount of memory used.
	* Most tools can output their results in SAM format, including
	AdjList, KAligner, ParseAligns and PathOverlap.

	abyss-pe:
	* New command, se-dot. Output a Graphviz dot file of the
	single-end assembly.

	ABYSS:
	* Handle multi-line FASTA sequences.
	* Report the amount of memory used.
	* Improve error messages for incorrectly-formatted FASTA files.
	* Bug fix. Improved handling of palindromes.

	PopBubbles:
	* Merge contigs after popping bubbles.
	* Bug fix. Do not pop bubbles resulting from palindromes.

	KAligner:
	* Report the amount of memory used.
	* New option, --sam. Output the alignments in SAM format.

	ParseAligns, DistanceEst:
	* Bug fix. The CIGAR string was oriented with respect to the
	query rather than with respect to the target, which is standard.

	AdjList, PathOverlap:
	* New option, --sam. Output the adjacency graph in SAM format.

	abyss-fixmate:
	* New program. Similar to samtools fixmate, but does not require
	that the input be sorted by query ID, although it is faster if it
	is sorted.

2010-07-12  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.1.
	* Handle reverse-forward oriented mate pair libraries.
	* Improved distance estimates, particularly with large fragment
	libraries.

	abyss-pe:
	* New commands:
	se-contigs: Assemble single-end contigs.
	pe-contigs: Assemble paired-end contigs (default).
	se-sam: Output a gzipped SAM file of the single-end assembly.
	se-bam: Ouptut a BAM file of the single-end assembly.
	pe-dot: Output a Graphviz dot file of the paired-end assembly.
	all: Sam as se-bam pe-contigs pe-dot.
	* Options for one particular library may be specified:
	lib='lib1 lib2' lib2_s=1000 lib2_n=25
	* Input sequence may come from an arbitrary command, which is
	useful to assemble a region of an aligned BAM file:
	in='<(samtools view genome.bam chr10)'

	ABYSS:
	* Bug fix. When reading SAM/BAM files, the quality format
	incorrectly defaulted to ASCII-64, when it should be ASCII-33.

	ABYSS-P:
	* May use the Intel MPI library.

	ParseAligns:
	* Count the number of forward-reverse, reverse-forward and
	forward-forward oriented alignments.

	DistanceEst:
	* Handle reverse-forward oriented mate pair libraries.
	* Improved distance estimates, particularly with large fragment
	libraries.
	* Remove duplicate mate pairs.
	* Print a pretty UTF-8 bar plot of the fragment-size distribution.
	* Multithreaded using OpenMP. The -j, --threads option specifies
	the number of threads to use.
	* Performance improvment.

	Overlap:
	* Handle cases when more than one gap occurs within the mate pair
	fragment size.

	SimpleGraph:
	* Performance improvment.

	MergePaths:
	* Handle the case when a circular sequence is assmembled into a
	single contig.

	abyss-tofastq:
	* New program. Convert qseq, export, SAM and BAM files to FASTA or
	FASTQ format. The files may be compressed with gz, bz2 or xz and
	may be tarred.

2010-05-25  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.2.0.
	* Scaffold over gaps in coverage and unresolved repetitive
	sequence using Ns.
	* Read sequence from SAM and BAM files.

	abyss-pe:
	* Set q=3 by default. Trim bases from the ends of reads whose
	quality is less than 3.
	* Do not store the .pair.gz file.
	* Generate a BAM file of the mate pairs that align to
	different contigs of the single-end assembly. Disabled by default.
	* Output a Graphviz dot file of the paired-end assembly.
	Disabled by default.
	* Store the bubbles in ${name}-bubbles.fa rather than bubbles.fa.
	* Store the indel bubbles in ${name}-indel.fa.
	* Bug fix for mawk.

	ABYSS:
	* Set -E0 when coverage is low (<2).

	ABYSS-P:
	* Remove the temporary files contigs-*.fa and snp-*.fa.

	PopBubbles:
	* Output in Graphviz dot format using --dot.

	KAligner:
	* Do not ignore sequences (reads or contigs) containing N.
	* Output SAM headers (but not SAM alignments).

	ParseAligns:
	* Output in SAM format.

	DistanceEst:
	* Input in SAM format.
	* Output in Graphviz dot format using --dot.

	Overlap:
	* Scaffold over gaps in coverage. Scaffolding can be disabled
	using the option --no-scaffold.
	* Merge contigs that overlap at simple repeats. These merges can
	be prevented using the option --no-merge-repeat.

	SimpleGraph:
	* Scaffold over repeats. Scaffolding can be disabled using the
	option --no-scaffold.

	MergePaths:
	* Merge paths containing ambiguous sequence.
	* Multithreaded using OpenMP. The -j, --threads option specifies
	the number of threads to use.

	MergeContigs:
	* Merge paths and contigs containing ambiguous sequence.

	PathOverlap:
	* Output in Graphviz dot format using --dot.

	Consensus:
	* Output the pileup in samtools format.

2010-02-15  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.1.2.

	ABYSS:
	* Read tar files including compressed tar files.
	* New parameter -b, --bubble-length=N. Pop bubbles shorter than
	N bp. The default is b=3*k.

	AdjList:
	* Include the contig coverage in the output.
	* The script abyss-adjtodot converts an ABySS adjacency file to
	GraphViz dot format.

	PopBubbles:
	* Pop bubbles resulting from indels.

	KAligner:
	* Synchronize the threads periodically (every ten thousand
	alignments by default) to ease the computational burden on
	ParseAligns. This synchronization can be disabled using --sync=0.
	* Use two threads by default.

	abyss-pe:
	* New parameter, b.
	* Use two threads by default.
	* The read length argument, l, is deprecated. To emulate the
	behaviour of ABySS 1.0.14 and older, set t=6*(l-k+1). The default
	is t=k.

2010-01-19  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.1.1.

	ABYSS:
	* Pop complex bubbles either completely or not at all. Bubble
	popping now completes in a single round.
	* Choose better (typically lower) default values for the
	parameters -e,--erode and -c,--coverage. The default threshold is
	the square root of the median k-mer coverage.

2009-12-18  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.1.0.
	* The output format of AdjList, DistanceEst and SimpleGraph has
	changed to be more humanly readable.

	ABYSS:
	* New options, -q, --trim-quality. Trim bases from the ends of
	reads whose quality is less than the specified threshold.
	--standard-quality: zero quality is `!' (33)
	default for FASTQ files
	--illumina-quality: zero quality is `@' (64)
	default for qseq and export files
	Thanks to Tony Raymond.

	SimpleGraph:
	* Multithreaded. The -j, --threads option specifies the number of
	threads to use.
	* Expand tandem repeats when it is possible to determine the exact
	number of the repeat.

	MergePaths:
	* Bug fix. A repeat that is larger than the fragment size could
	be misassembled. Thanks to Tony Raymond.

	abyss-pe:
	* Determine the parameter j (number of threads) by finding the
	number of slots allocated on the head node in the PE_HOSTFILE.
	* Store the k-mer coverage histogram in coverage.hist.

2009-11-13  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.16.
	* Improve the performance and memory usage of KAligner and
	AdjList, particularly for very large data sets.

	KAligner:
	* Improve memory usage when maxk is 32 or 96. No change when maxk
	is the default 64.
	* New option, -i, --ignore-multimap. Ignore any duplicate k-mer in
	the target sequence. Thanks to Tony Raymond.

	AdjList:
	* Improve performance for very large data sets.

	ParseAligns:
	* For reads whose ID begins with `SRR', expect that the forward
	and reverse read have identical ID and no suffix, such as
	/1 and /2.

2009-10-19  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.15.

	ABYSS:
	* New options, -e, --erode and -E, --erode-strand.
	The parameter e erodes bases at the ends of blunt contigs with
	coverage less than the specified threshold.
	The parameter E erodes bases at the ends of blunt contigs with
	coverage less than the specified threshold on either strand.
	* New feature. If the parameters e and c are not specified,
	attempt to choose appropriate values based on the observed k-mer
	coverage. This feature will work best for higher coverage data.
	For lower coverage data, setting e=c=2 is reasonable.
	* New option, --trim-masked. Removed masked (lower case) sequence
	at the beginning and end of the read. Disable with
	--no-trim-masked.
	* The read length, l, is an optional parameter. If the read length
	is specified, the trim parameter, t, will default to 6*(l-k+1), as
	before. If the read length is not specified, t will be set to the
	same value as k. For longer reads or when k is less than 85% of l,
	it should not be necessary to specify l. The parameter t may be
	specified directly if desired.

	DistanceEst:
	* Bug fix. The standard deviation could be calculated incorrectly
	for larger numbers, particularly for libraries with large fragment
	sizes. Thanks to Tony Raymond.

	Overlap:
	* Bug fix. If Overlap found mate pairs on the same contig with
	incorrect orientation, it would generate a misassembled contig.
	These misassembled contigs are easily identified in the
	xxx-3-overlap.fa file. The two contigs IDs, in the fourth and
	fifth column, will be identical.
	* New option, --mask-repeat. If two contigs are joined by mate
	pairs and are found to overlap by a simple repeat so that the
	exact number of the repeat is unknown, join the contigs estimating
	the number of the repeat, and mask (lower case) the repeat
	sequence. This feature is disabled by default.

	abyss-pe:
	* Use gunzip -c rather than zcat for portability.

	configure:
	* New option, --enable-mpich. Use the MPICH2 MPI library.

2009-09-08  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.14.
	* Read files compressed with xzip (.xz) and compress (.Z).

	abyss-pe:
	* Assemble multiple libraries with different fragment sizes.
	* New manual page.

	ABYSS:
	* Don't necessarily discard reads that contain an N. Keep those
	k-mer that do not contain an N.

	ABYSS-P:
	* Serially renumber the contigs output by ABYSS-P using awk.

2009-08-26  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.13.
	* Read files compressed with gzip (.gz) or bzip2 (.bz2).

	ABYSS-P:
	* Bug fix. Fix a race condition in the erosion algorithm.

2009-08-18  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.12.

	abyss-pe:
	* Both ABYSS and KAligner are run only once per assembly, which
	speeds up the paired-end assembly by nearly a factor of two.
	* The k-mer coverage information is correct in every contig file.
	* A new parameter, cs, converts colour-space contigs to nucleotide
	contigs using Consensus.
	* A new parameter, ABYSS_OPTIONS, may be used to disable chastity
	filtering by specifying ABYSS_OPTIONS=--no-chastity.

	ABYSS:
	* Read files in export format, which is similar to qseq format.
	* Discard reads that failed the chastity filter. Use the
	--no-chastity option to retain these unchaste reads. Chastity
	filtering affects only qseq- and export formatted-files.
	* Remove low-coverage contigs within ABYSS rather than filtering
	using awk and reassembling.
	* Support big-endian architecture machines.

	KAligner:
	* A new option, -m or --multimap, specifies that a duplicate k-mer
	may be seen in the target sequence. By default, every k-mer in the
	target sequence must be unique.
	* A new option, --seq, prints the read sequence of each alignment.

	Overlap:
	* A new option, --scaffold, fills the gap between two blunt
	contigs with Ns. This feature is disabled by default.

	Consensus:
	* Call the consensus sequence for each contig based on the
	alignment of reads to contigs.
	* Convert colour-space contigs to nucleotide contigs.
	* Written by Tony Raymond.

2009-07-21  Shaun Jackman  <sjackman@bcgsc.ca>

	* 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  <sjackman@bcgsc.ca>

	* Release version 1.0.10.

	abyss-pe:
	* Start an MPI ABySS assembly if the np option is specified.

	ABYSS:
	* For a non-parallel assembly, allocate more hash buckets to allow
	for large single-machine jobs.
	* Print the hash load during the loading process.

	KAligner:
	* Output the IDs of reads that do not align.
	* Print a progress report of the number of reads aligned.

	ParseAligns:
	* To reduce memory usage, do not track reads that did not align.
	KAligner and ParseAligns should now be able to handle any number
	of reads in a single run.

	MergePaths:
	* Number paired-end contigs so that their IDs do not overlap with
	the single-end contigs. If a single-end contig is not used in a
	paired-end contig, its ID will not change.
	* Merge overlapping paired-end contigs that were previously
	being missed in some situations.

	configure:
	* Print a warning if Google sparsehash was not found.

2009-05-15  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.9.

	abyss-pe:
	* Allow multiple input files specified by the parameter `in'.
	* Support reading FASTA or FASTQ file formats.

	KAligner:
	* Support using Google sparsehash to reduce memory usage.
	Google sparsehash does not provide a multimap, so KAligner built
	using Google sparsehash cannot handle a duplicate k-mer in the
	reference sequence. It will print an error message and die if a
	duplicate k-mer is encountered. If Google sparsehash is not used,
	the standard STL multimap will be used which does permit duplicate
	k-mer.
	* Support reading the query sequence from standard input.

	ParseAligns:
	* Significantly reduce memory usage if the mate reads are
	encountered one after the next in the same file.

2009-04-02  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.8.
	* Bug fix. Fix the undefined behaviour causing the error
	Assertion `marked == split' failed.

2009-03-31  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.7.
	* Use a mark-and-sweep trimming algorithm to remove errors at the
	ends of blunt contigs.
	* The parallel (ABYSS-P) trimming algorithm is now deterministic;
	it will produce the same result every time. In addition, the
	result of the parallel trimming algorithm is identical to the
	result of the non-parallel trimming algorithm.
	* Start trimming branches at length 1, previously 2.
	* Bug fix in ABYSS-P. Repeat sequences of k-1 bases could
	potentially be misassembled. Use a mark-and-sweep algorithm to
	split ambiguous edges before contig generation. The previous
	algorithm was not deterministic.
	* Reduce memory usage by 200 MB by removing the MPI transmit
	buffer.
	* Bug fix in ABYSS-P. Fix an additional race condition in the
	erosion algorithm.

2009-03-24  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.6.
	* Bug fix. Fix a race condition in the erosion algorithm.
	* For the parallel program (ABYSS-P), after bubble popping perform
	as many trimming rounds as necessary to remove all the tips, as
	the non-parallel program does.
	* New script, abyss2afg, to create an AMOS AFG assembly.

2009-03-11  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.5.
	* Portability fixes. Tested with g++ 4.3.3.

2009-03-04  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.4.

	ABYSS:
	* Remove the need to specify a -e,--erode parameter by improving
	the erosion algorithm to complete in a single pass.
	* Remove the default limit on the maximum number of bubble
	popping rounds. A limit may be specified using -b,--bubbles.
	* Generate a warning if an input file is empty, but do not die.
	* When using a Google sparsehash, allocate room for 100 million
	k-mers.
	* Increase the maximum FASTA line length from 64 kB to 256 kB.
	* Require only one of either -l,--read-length or -t,--trim-length
	to be specified.
	* Allow read pairs to be named `_forward' and `_reverse'.
	* Ensure that exactly k-1 bases of context is given on each side
	of the bubble sequence. Previously, one side would have k bases of
	context, and the other side would have k-1 bases.
	* Add command line options to each of the paired-end programs.

	ABYSS-P:
	* Use Open MPI as the default MPI library.
	* Do not link against the Open MPI C++ library.

	abyss-pe:
	* Use pipes where possible to avoid intermediate files.
	* The semantics of the n argument have changed. See DistanceEst
	-n,--npairs below.

	SimpleGraph:
	* If more than one path is found but only one meets all of the
	constraints, use it.
	* Allow for some constant error in distance estimates that does
	not decrease with the number of samples. The expected fragment
	size seems to vary with genomic coordinate to a certain degree.
	So, the distribution of fragment size spanning two given contigs
	may differ from the empirical distribution by a roughly constant
	offset.

	DistanceEst:
	* The semantics of the -n,--npairs option has changed.
	Require at least NPAIRS pairs between contigs (>= NPAIRS).
	Previously, required strictly more than NPAIRS pairs between
	contigs (> NPAIRS).
	* Give the estimated error to a single decimal place.
	* When counting the number of pairs that join two contigs, only
	count pairs that fit the empirical distribution.
	* When deciding whether the pairs joining two contigs are
	inconsistent in sense, require NPAIRS read pairs joining two
	contigs in each sense before considering the pair data to be
	inconsistent.

	ParseAligns:
	* Measure fragments in total size, not alignment distance.
	* Allow a read that spans two contigs to be used in distance
	estimates.
	* Add the -h,--hist option to produce a histogram.
	* Bug fix. When measuring the empirical fragment size, ensure that
	the sense of the alignments is correct. Output a negative fragment
	size if the reverse read aligns ahead of the forward read.
	* Bug fix. Miscalculated the fragment size estimate between two
	contigs if they did not have the same sense and one contig
	required flipping. It was possible to see one distance estimate
	from contig A to contig B and a differing estimate from contig B
	to contig A. Typically, the distance estimate would be off by
	one.

2009-01-23  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.3.
	* Merge contigs that ended due to a lack of coverage, but which
	are connected by paired-end reads and overlap unambiguously.
	* Track the multiplicity the sense and antisense strand
	separately. Erode the end of a blunt contig until it is
	represented by both strands.
	* Ignore the case of the nucleotide sequence of a FASTA file.
	* Increase the maximum FASTA line length from 1 kB to 64 kB to
	allow loading contigs.
	* Output the path through the single-end contigs in the comment
	field of the paired-end contig.
	* In the paired-end driver script, abyss-pe,
	Implement a coverage cutoff, c.
	Pass the erosion parameter, e, to the single-end assembler.

2008-11-21  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.2.
	* Terminate contig extension at palindromic k-mers.
	* If erosion (-e,--erode) is enabled, remove the tips of blunt
	contigs that are represented only once.

2008-11-07  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.1.
	* Portability improvements to compile for Mac OS X.

2008-08-07  Shaun Jackman  <sjackman@bcgsc.ca>

	* Release version 1.0.
