2013-07-10  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130710 (tag:alpha)

	* fix BED style output format of callpeak module:

	1) without --broad: narrowPeak (BED6+4) and BED for summit will be
	the output. Old BED format file won't be saved.

	2) with --broad: broadPeak (BED6+3) for broad region and
	gappedPeak (BED12+3) for chained enriched regions will be the
	output. Old BED format, narrowPeak format, summit file won't be
	saved.

	* bdgcmp now can accept list of methods to calculate scores. So
	you can run it once to generate multiple types of scores. Thank
	Jon Urban for this suggestion!

	* C codes are re-generated through Cython 0.19.1.

2013-05-21  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130520 (tag:alpha)

	* broad peak calling modules are modified in order to report all
	relexed regions even there is no strong enrichment inside.

2013-05-01  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130501 (tag:alpha)

	* Memory usage is decreased to about 1/4-1/5 of previous usage
	Now, the internal data structure and algorithm are both
	re-organized, so that intermediate data wouldn't be saved in
	memory. Intead they will be calculated on the fly. New MACS2 will
	spend longer time (1.5 to 2 times) however it will use less memory
	so can be more usable on small mem servers.

	* --seed option is added to callpeak and randsample commands
	Thank Mathieu Gineste for this suggestion!

2013-03-05  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130306 (tag:alpha)

	* diffpeak module New module to detect differential binding sites
	with more statistics.

	* Introduced --refine-peaks
	Calculates reads balancing to refine peak summits

	* Ouput file names prefix
	Correct encodePeak to narrowPeak, broadPeak to bed12. 

2012-09-13 Benjamin Schiller <benjamin.schiller@ucsf.edu>,  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS version 2.0.10 (tag:alpha not released)

	* Introduced BAMPEParser
	Reads PE data directly, requires bedtools for now

	* Introduced --call-summits
	Uses signal processing methods to call overlapping peaks

	* Added --no-trackline
	By default, files have descriptive tracklines now

	* new refinepeak command (experimental)
	This new function will use a similar method in SPP (wtd), to
	analyze raw tag distribution in peak region, then redefine the
	peak summit where plus and minus tags are evenly distributed
	around.

	* Changes to output *
	cPeakDetect.pyx has full support for new print/write methods and
	--call-peaks, BAMPEParser, and use of paired-end data

	* Parser optimization

	cParser.pyx is rewritten to use io.BufferedReader to speed
	up. Speed is doubled.

	Code is reorganized -- most of functions are inherited from
	GenericParser class.

	* Use cross-correlation to calculate fragment size

	First, all pairs will be used in prediction for fragment
	size. Previously, only no more than 1000 pairs are used. Second,
	cross-correlation is used to find the best phase difference
	between + and - tag pileups.

	* Speed up p-value and q-value calculation

	This part is ten times faster now. I am using a dictionary to
	cache p-value results from Poisson CDF function. A bit more memory
	will be used to increase speed. I hope this dictionary would not
	explode since the possible pairs of ChIP signal and control lambda
	are hugely redundant. Also, I rewrited part of q-value
	calculation.

	* Speed up peak detection

	This part is about hundred of times faster now.  Optimizations
	include using Numpy functions as much as possible, and making loop
	body as small as possible.

	* Post-processing on differential calls

	After macs2diff finds differential binding sites between two
	conditions, it will try to annotate the peak calls from one of two
	conditions, describe the changes ...

	* Fragment size prediction in macs2diff

	Now by default, macs2diff will try to use the average fragment
	size from both condition 1 and condition 2 for tag extension and
	peak calling. Previously, by default, it will use different sizes
	unless --nomodel is specified.

	Technically, I separate model building processes out. So macs2diff
	will build fragment sizes for condition 1 and 2 in parallel (2
	processes maximum), then perform 4-way comparisons in parallel (4
	processes maximum).

	* Diff score

	Combine two p/qscore tracks together. At regions where condition 1
	is higher than condition 2, score would be positive, otherwise,
	negative.

	* SAMParser and BAMParser

	Bug fixed for paired-end sequencing data.

	* BedGraph.pyx

	Fixed a bug while calling peaks from BedGraph file. It previously
	mistakenly output same peaks multiple times at the end of
	chromosome.

2011-11-2  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS version 2.0.9 (tag:alpha)

	* Auto fixation on predicted d is turned off by default!

	Previous --off-auto is now default. MACS will not automatically
	fix d less than 2 times of tag size according to
	--shiftsize. While tag size is getting longer nowadays, it would
	be easier to have d less than 2 times of tag size, however d may
	still be meaningful and useful. Please judge it using your own
	wisdom.

	* Scaling issue

	Now, the default scaling while treatment and input are unbalanced
	has been adjusted. By default, larger sample will be scaled down
	linearly to match the smaller sample. In this way, background
	noise will be reduced more than real signals, so we expect to have
	more specific results than the other way around (i.e. --to-large
	is set).

	Also, an alternative option to randomly sample larger data
	(--down-sample) is provided to replace default linear
	scaling. However, this option will cause results irresproducible,
	so be careful. 

	* randsample script

	A new script 'randsample'  is added, which can randomly sample
	certain percentage or number of tags.

	* Peak summit

	Now, MACS will decide peak summits according to pileup height
	instead of qvalue scores. In this way, the summit may be more
	accurate. 

	* Diff score

	MACS calculate qvalue scores as differential scores. When compare
	two conditions (saying A and B), the maximum qscore for comparing
	A to B -- maxqscore_a2b, and for comparing B to A --maxqscore_b2a
	will be computed. If maxqscore_a2b is bigger, the diff score is
	+maxqscore_a2b, otherwise, diff score is -1*maxqscore_b2a.

2011-09-15  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS version 2.0.8 (tag:alpha)

	* bin/macs2, bin/bdgbroadcall, MACS2/IO/cScoreTrack.pyx, MACS2/IO/cBedGraph.pyx

	New script bdgbroadcall and the extra option '--broad' for macs2
	script, can be used to call broad regions with a loose cutoff to
	link nearby significant regions. The output is represented as
	BED12 format.

	* MACS2/IO/cScoreTrack.pyx

	Fix q-value calculation to generate forcefully monotonic values.

	* bin/eland*2bed, bin/sam2bed and bin/filterdup

	They are combined to one more powerful script called
	"filterdup". The script filterdup can filter duplicated reads
	according to sequencing depth and genome size. The script can also
	convert any format supported by MACS to BED format.

2011-08-21  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS version 2.0.7 (tag:alpha)

	* bin/macsdiff renamed to bin/bdgdiff

	Now this script will work as a low-level finetuning tool as bdgcmp
	and bdgpeakcall.

	* bin/macs2diff

	A new script to take treatment and control files from two
	condition, calculate fragment size, use local poisson to get
	pvalues and BH process to get qvalues, then combine 4-ways result
	to call differential sites.

	This script can use upto 4 cpus to speed up 4-ways calculation. (
	I am trying multiprocessing in python. )

	* MACS2/Constants.py, MACS2/IO/cBedGraph.pyx,
	MACS2/IO/cScoreTrack.pyx, MACS2/OptValidator.py,
	MACS2/PeakModel.py, MACS2/cPeakDetect.pyx

	All above files are modified for the new macs2diff script.

	* bin/macs2, bin/macs2diff, MACS2/OptValidator.py

	Now q-value 0.01 is the default cutoff. If -p is specified,
	p-value cutoff will be used instead.

2011-07-25  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.6 (tag:alpha)

	* bin/macsdiff

	A script to call differential regions. A naive way is introduced
	to find the regions where:

	1. signal from condition 1 is larger than input 1 and condition 2 --
	unique region in condition 1;
	2. signal from condition 2 is larger than input 2 and condition 1
	-- unique region in condition 2;
	3. signal from condition 1 is larger than input 1, signal from
	condition 2 is larger than input 2, however either signal from
	condition 1 or 2 is not larger than the other.

	Here 'larger' means the pvalue or qvalue from a Poisson test is
	under certain cutoff.

	(I will make another script to wrap up mulitple scripts for
	differential calling)

2011-07-07  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.5 (tag:alpha)

	* bin/macs2, MACS2/cPeakDetect.py, MACS2/IO/cScoreTrack.pyx,
	MACS2/IO/cPeakIO.pyx

	Use hash to store peak information. Add back the feature to deal
	with data without control.

	Fix bug which incorrectly allows small peaks at the end of
	chromosomes.

	* bin/bdgpeakcall, bin/bdgcmp

	Fix bugs. bdgpeakcall can output encodePeak format.

2011-06-22  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS version 2.0.4 (tag:alpha)

	* cPeakDetect.py

	Fix a bug, correctly assign lambda_bg while --to-small is
	set. Thanks Junya Seo!

	Add rank and num of bp columns to pvalue-qvalue table.

	* cScoreTrack.py

	Fix bugs to correctly deal with peakless chromosomes. Thanks
	Vaibhav Jain!

	Use AFDR for independent tests instead.

	* encodePeak

	Now MACS can output peak coordinates together with pvalue, qvalue,
	summit positions in a single encodePeak format (designed for
	ENCODE project) file. This file can be loaded to UCSC
	browser. Definition of some specific columns are: 5th:
	int(-log10pvalue*10), 7th: fold-change, 8th: -log10pvalue, 9th:
	-log10qvalue, 10th: relative summit position to peak start.


2011-06-19  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS version 2.0.3 (tag:alpha)

	* Rich output with qvalue, fold enrichment, and pileup height

	Calculate q-values using a refined Benjamini–Hochberg–Yekutieli
	procedure:

	http://en.wikipedia.org/wiki/False_discovery_rate#Dependent_tests

	Now we have a similiar xls output file as before. The differences
	from previous file are:

	1. Summit now is absolute summit, instead of relative summit
	   position;
	2. 'Pileup' is previous 'tag' column. It's the extended fragment
	   pileup at the peak summit;
	3. We now use '-log10(pvalue)' instead of '-10log10(pvalue)', so
	   5.00 means 1e-5, simple and less confusing.
	4. FDR column becomes '-log10(qvalue)' column.
	5. The pileup, -log10pvalue, fold_enrichment and -log10qvalue are
	   the values at the peak summit.

	* Extra output files

	NAME_pqtable.txt contains pvalue and qvalue relationships.

	NAME_treat_pvalue.bdg and NAME_treat_qvalue.bdg store -log10pvalue
	and -log10qvalue scores in BedGraph format. Nearby regions with
	the same value are not merged.

	* Separation of FeatIO.py

	Its content has been divided into cPeakIO.pyx, cBedGraph.pyx, and
	cFixWidthTrack.pyx. A modified bedGraphTrackI class was
	implemented to store pileup, local lambda, pvalue, and qvalue
	alltogether in cScoreTrack.pyx.

	* Experimental option --half-ext

	Suggested by NPS algorithm, I added an experimental option
	--half-ext to let MACS only extends ChIP fragment around its
	middle point for only 1/2 d.

2011-06-12  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS version 2.0.2 (tag:alpha)

	* macs2

	Add an error check to see if there is no common chromosome names
	from treatment file and control file

	* cPeakDetect.pyx, cFeatIO.pyx, cPileup.pyx

	Reduce memory usage by removing deepcopy() calls.

	* Modify README documents and others.

2011-05-19  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS Version 2.0.1 (tag:alpha)

	* cPileup.pyx, cPeakDetect.pyx and peak calling process

	Jie suggested me a brilliant simple method to pileup fragments
	into bedGraph track. It works extremely faster than the previous
	function, i.e, faster than MACS1.3 or MACS1.4. So I can include
	large local lambda calculation in MACSv2 now. Now I generate three
	bedGraphs for d-size local bias, slocal-size and llocal-size local
	bias, and calculate the maximum local bias as local lambda
	bedGraph track.

	Minor: add_loc in bedGraphTrackI now can correctly merge the
	region with its preceding region if their value are the same.

	* macs2

	Add an option to shift control tags before extension. By default,
	control tags will be extended to both sides regardless of strand
	information.

2011-05-17  Tao Liu  <taoliu@jimmy.harvard.edu>
	MACS Version 2.0.0 (tag:alpha)

	* Use bedGraph type to store data internally and externally.

	We can have theoretically one-basepair resolution profiles. 10
	times smaller in filesize and even smaller after converting to
	bigWig for visualization.

	* Peak calling process modified. Better peak boundary detection.

	Extend ChIP tag to d, and pileup to have a ChIP bedGraph. Extend
	Control tag to d and 1,000bp, and pileup to two bedGraphs. (1000bp
	one will be averaged to d size) Then calculate the maximum value
	of these two tracks and a global background, to have a
	local-lambda bedGraph.

	Use -10log10poisson_pvalue as scores to generate a score track
	before peak calling.

	A general peak calling based on a score cutoff, min length of peak
	and max gap between nearby peaks.

	* Option changes.

	Wiggle file output is removed. Now we only support bedGraph
	output. The generation of bedGraph is highly recommended since it
	will not cost extra time. In other words, bedGraph generation is
	internally run even you don't want to save bedGraphs on disk, due
	to the peak calling algorithm in MACS v2.

	* cProb.pyx

	We now can calculate poisson pvalue in log space so that the score
	(-10*log10pvalue) will not have a upper limit of 3100 due to
	precision of float number.

	* Cython is adopted to speed up Python code.

2011-02-28  Tao Liu  <taoliu@jimmy.harvard.edu>
	Small fixes

	* Replaced with a newest WigTrackI class and fixed the wignorm script.

2011-02-21  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.4.0rc2 (Valentine)

	* --single-wig option is renamed to --single-profile

	* BedGraph output with --bdg or -B option.

	The BedGraph output provides 1bp resolution fragment pileup
	profile. File size is smaller than wig file. This option can be
	combined with --single-profile option to produce a bedgraph file
	for the whole genome. This option can also make --space,
	--call-subpeaks invalid.

	* Fix the description of --shiftsize to correctly state that the
	value is 1/2 d (fragment size).

	* Fix a bug in the call to __filter_w_control_tags when control is
	not available.

	* Fix a bug on --to-small option. Now it works as expected.

	* Fix a bug while counting the tags in candidate peak region, an
	extra tag may be included. (Thanks to Jake Biesinger!)

	* Fix the bug for the peaks extended outside of chromosome
	start. If the minus strand tag goes outside of chromosome start
	after extension of d, it will be thrown out.

	* Post-process script for a combined wig file:

	The "wignorm" command can be called after a full run of MACS14 as
	a postprocess. wignorm can calculate the local background from the
	control wig file from MACS14, then use either foldchange,
	-10*log10(pvalue) from possion test, or difference after asinh
	transformation as the score to build a single wig track to
	represent the binding strength. This script will take a
	significant long time to process.

	* --wigextend has been obsoleted.

2010-09-21  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.4.0rc1 (Starry Sky)

	* Duplicate reads option

	--keep-dup behavior is changed. Now user can specify how many
	reads he/she wants to keep at the same genomic location. 'auto' to
	let MACS decide the number based on binomial distribution, 'all'
	to let MACS keep all reads.

	* pvalue and FDR fixes (Thanks to Prof. Zhiping Weng)

	By default, MACS will now scale the smaller dataset to the bigger
	dataset. For instance, if IP has 10 million reads, and Input has 5
	million, MACS will double the lambda value calculated from Input
	reads while calling BOTH the positive peaks and negative
	peaks. This will address the issue caused by unbalanced numbers of
	reads from IP and Input. If --to-small is turned on, MACS will
	scale the larger dataset to the smaller one. So from now on, if d
	is fixed, then the peaks from a MACS call for A vs B should be
	identical to the negative peaks from a B vs A.

2010-09-01  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.4.0beta (summer wishes)

	* New features

	** Model building

	The default behavior in the model building step is slightly
	changed. When MACS can't find enough pairs to build model
	(implemented in alpha version) or the modeled fragment length is
	less than 2 times of tag length (implemented in beta version),
	MACS will use 2 times of --shiftsize value as fragment length in
	the later analysis. --off-auto can turn off this default behavior.

	** Redundant tag filtering

	The IO module is rewritten. The redundant tag filtering process
	becomes simpler and works as promise. The maximum allowed number
	of tags at the exact same location is calculated from the
	sequencing depth and genome size using a binomial distribution,
	for both TREAMENT and CONTROL separately. ( previously only
	TREATMENT is considered ) The exact same location means the same
	coordination and the same strand. Then MACS will only keep at most
	this number of tags at the exact same location in the following
	analysis. An option --keep-dup can let MACS skip the filtering and
	keep all the tags. However this may bring in a lot of sequencing
	bias, so you may get many false positive peaks.

	** Single wiggle mode

	First thing to mention, this is not the score track that I
	described before. By default, MACS generates wiggle files for
	fragment pileup for every chromosomes separately. When you use
	--single-wig option, MACS will generate a single wiggle file for
	all the chromosomes so you will get a wig.gz for TREATMENT and
	another wig.gz for CONTROL if available.

	** Sniff -- automatic format detection

	Now, by default or "-f AUTO", MACS will decide the input file
	format automatically. Technically, it will try to read at most
	1000 records for the first 10 non-comment lines. If it succeeds,
	the format is decided. I recommend not to use AUTO and specify the
	right format for your input files, unless you combine different
	formats in a single MACS run.

	* Options changes

	--single-wig and --keep-dup are added. Check previous section in
	ChangeLog for detail.

	-f (--format) AUTO is now the default option.

	--slocal default: 1000
	--llocal default: 10000

	* Bug fixed

	Setup script will stop the installation if python version is not
	python2.6 or python2.7.

	Local lambda calculation has been changed back. MACS will check
	peak_region, slocal( default 1K) and llocal (default 10K) for the
	local bias. The previous 200bps default will cause MACS misses
	some peaks where the input bias is very sharp.

	sam2bed.py script is corrected.

	Relative pos in xls output is fixed.

	Parser for ELAND_export is fixed to pass some of the no match
	lines. And elandexport2bed.py is fixed too. ( however I can't
	guarantee that it works on any eland_export files. )

2010-06-04  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.4.0alpha2 (be smarter)

	* Options changes

	--gsize now provides shortcuts for common genomes, including
	human, mouse, C. elegans and fruitfly.

	--llocal now will be 5000 bps if there is no input file, so that
	local lambda doesn't overkill enriched binding sites.

2010-06-02  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.4alpha (be smarter)
	
	* Options changes

	--tsize option is redesigned. MACS will use the first 10 lines of
	the input to decide the tag size. If user specifies --tsize, it
	will override the auto decided tsize.

	--lambdaset is replaced by --slocal and --llocal which mean the
	small local region and large local region. 

	--bw has no effect on the scan-window size now. It only affects the
	paired-peaks model process. 
	
	* Model building

	During the model building, MACS will pick out the enriched regions
	which are not too high and not too low to build the paired-peak
	model. Default the region is from fold 10 to fold 30. If MACS
	fails to build the model, by default it will use the nomodel
	settings, like shiftsize=100bps, to shift and extend each
	tags. This behavior can be turned off by '--off-auto'.

	* Output files

	An extra file including all the summit positions are saved in
	*_summits.bed file. An option '--call-subpeaks' will invoke
	PeakSplitter developed by Mali Salmon to split wide peaks into
	smaller subpeaks.
	
	* Sniff ( will in beta )

	Automatically recognize the input file format, so use can combine
	different format in one MACS run.

	Not implemented features/TODO:
	
	* Algorithms ( in near future? )

	MACS will try to refine the peak boundaries by calculating the
	scores for every point in the candidate peak regions. The score
	will be the -10*log(10,pvalue) on a local poisson distribution. A
	cutoff specified by users (--pvalue) will be applied to find the
	precise sub-peaks in the original candidate peak region. Peak
	boudaries and peak summits positions will be saved in separate BED
	files.

	* Single wiggle track ( in near future? )

	A single wiggle track will be generated to save the scores within
	candidate peak regions in the 10bps resolution. The wiggle file
	is in fixedStep format.


2009-10-16  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.7.1 (Oktoberfest, bug fixed #1)
	
	* bin/Constants.py

	Fixed typo. FCSTEP -> FESTEP

	* lib/PeakDetect.py

	The 'femax' attribute bug is fixed

2009-10-02  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.7 (Oktoberfest)
	
	* bin/macs, lib/PeakDetect.py, lib/IO/__init__.py, lib/OptValidator.py

	Enhancements by Peter Chines:

	1. gzip files are supported. 
	2. when --diag is on, user can set the increment and endpoint for
	fold enrichment analysis by setting --fe-step and --fe-max.

	Enhancements by Davide Cittaro:

	1. BAM and SAM formats are supported.
	2. small changes in the header lines of wiggle output.

	Enhancements by Me:
	1. I added --fe-min option;
	2. Bowtie ascii output with suffix ".map" is supported.
	
	Bug fixed:

	1. --nolambda bug is fixed. ( reported by Martin in JHU )
	2. --diag bug is fixed. ( reported by Bogdan Tanasa )
	3. Function to remove suffix '.fa' is fixed. ( reported by Jeff Johnston )
	4. Some "fold change" have been changed to "fold enrichment".

2009-06-10  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.6.1 (default parameter change)
	
	* bin/macs, lib/PeakDetect.py

	"--oldfdr" is removed. The 'oldfdr' behaviour becomes
	default. "--futurefdr" is added which can turn on the 'new' method
	introduced in 1.3.6. By default it's off.

	* lib/PeakDetect.py

	Fixed a bug. p-value is corrected a little bit.
	

2009-05-11  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.6 (Birthday cake)
	
	* bin/macs

	"track name" is added to the header of BED output file.

	Now the default peak detection method is to consider 5k and 10k
	nearby regions in treatment data and peak location, 1k, 5k, and
	10k regions in control data to calculate local bias. The old
	method can be called through '--old' option.

	Information about how many total/unique tags in treatment or
	control will be saved in final .xls output.

	* lib/IO/__init__.py

	".fa" will be removed from input tag alignment so only the
	chromosome names are kept.

	WigTrackI class is added for Wiggle like data structure. (not used
	now)

	The parser for ELAND multi PET files has been fixed. Now the 5'
	tag position for a pair will be kept, whereas in the previous
	version, the middle points are kept.

	* lib/IO/BinKeeper.py

	BinKeeperI class is inspired by Jim Kent's library for UCSC genome
	browser, which can quickly access certain region for values in a
	large wiggle like data file. (not used now)

	* lib/OptValidator.py

	typo fixed.

	* lib/PeakDetect.py

	Now the default peak detection method is to consider 5k and 10k
	nearby regions in treatment data and peak location, 1k, 5k, and
	10k regions in control data to calculate local bias. The old
	method can be called through '--old' option.

	Two columns have beed added to BED output file. 4th column: peak
	name; 5th column: peak score using -10log(10,pvalue) as score.

	* setup.py

	Add support to build a Mac App through 'setup.py py2app', or a
	Windows executable through 'setup.py py2exe'. You need to install
	py2app or py2exe package in order to use these functions.

2009-02-12  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.5 (local lambda fixed, typo fixed, model figure improved)
	
	* PeakDetect.py

	Now, besides 1k, 5k, 10k, MACS will also consider peak size region
	in control data to calculate local lambda for each peak. Peak
	calling results will be slightly different with previous version,
	beware!

	* OptValidator.py

	Typo fixed, ELANDParser -> ELANDResultParser

	* OutputWriter.py

	Now, modeled d value will be shown on the model figure.

2009-01-06  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.4 (Happy New Year Version, bug fixed, ELAND multi/PET support)
	
	* macs, IO/__init__.py, PeakDetect.py

	Add support for ELAND multi format. Add support for Pair-End
	experiment, in this case, 5'end and 3'end ELAND multi format files
	are required for treatment or control data. See 00README file for
	detail.

	Add wigextend option.

	Add petdist option for Pair-End Tag experiment, which is the best
	distance between 5' and 3' tags.

	* PeakDetect.py

	Fixed a bug which cause the end positions of every peak region
	incorrectly added by 1 bp. ( Thanks Mali Salmon!)

	* OutputWriter.py
	
	Fix bugs while generating wiggle files. The start position of
	wiggle file is set to 1 instead of 0.

	Fix a bug that every 10M bps, signals in the first 'd' range are
	lower than actual. ( Thanks Mali Salmon!)


2008-12-03  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.3 (wiggle bugs fixed)
	
	* OutputWriter.py

	Fix bugs while generating wiggle files. 1. 'span=' is added to
	'variableStep' line; 2. previously, every 10M bps, the coordinates
	were wrongly shifted to the right for 'd' basepairs.

	* macs, PeakDetect.py

	Add an option to save wiggle files on different resolution.
	
2008-10-02  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.2 (tiny bugs fixed)

	* IO/__init__.py
	
	Fix 65536 -> 65535. ( Thank Joon) 
	
	* Prob.py
	
	Improved for binomial function with extra large number. Imported
	from Cistrome project.
	
	* PeakDetect.py

	If treatment channel misses reads in some chromosome included in
	control channel, or vice versa, MACS will not exit. (Thank Shaun
	Mahony)

	Instead, MACS will fake a tag at position -1 when calling
	treatment peaks vs control, but will ignore the chromosome while
	calling negative peaks.

2008-09-04  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3.1 (tiny bugs fixed version)

	* Prob.py
	
	Hyunjin Gene Shin contributed some codes to Prob.py. Now the
	binomial functions can tolerate large and small numbers.
	
	* IO/__init__.py

	Parsers now split lines in BED/ELAND file using any
	whitespaces. 'track' or 'browser' lines will be regarded as
	comment lines. A bug fixed when throwing StrandFormatError. The
	maximum redundant tag number at a single position can be no less
	than 65536.

	
2008-07-15  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.3 (naming clarification version)

	* Naming clarification changes according to our manuscript:

	'frag_len' is changed to 'd'.

	'fold_change' is changed to 'fold_enrichment'.
	
	Suggest '--bw' parameter to be determined by users from the real
	sonication size.

	Maximum FDR is 100% in the output file.

	And other clarifications in 00README file and the documents on the
	website.
	
	* IO/__init__.py
	If the redundant tag number at a single position is over 32767,
	just remember 32767, instead of raising an overflow exception.
	
	* setup.py
	fixed a typo.

	* PeakDetect.py
	Bug fixed for diagnosis report.
	

2008-07-10  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.2.2gamma

	* Serious bugs fix: 

	Poisson distribution CDF and inverse CDF functions are
	corrected. They can produce right results even for huge lambda
	now. So that the p-value and FDR values in the final excel sheet
	are corrected.

	IO package now can tolerate some rare cases; ELANDParser in IO
	package is fixed. (Thank Bogdan)

	* Improvement:

	Reverse paired peaks in model are rejected. So there will be no
	negative 'frag_len'. (Thank Bogdan)

	* Features added:
	
	Diagnosis function is completed. Which can output a table file for
	users to estimate their sequencing depth.


2008-06-30  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.2
	
	* Probe.py is added!  

	GSL is totally removed from MACS. Instead, I have implemented the
	CDF and inverse CDF for poisson and binomial distribution purely
	in python.

	* Constants.py is added!

	Organize constants used in MACS in the Constants.py file.

	* All other files are modified!

	Foldchange calculation is modified. Now the foldchange only be
	calculated at the peak summit position instead of the whole peak
	region. The values will be higher and more robust than before.

	Features added:

	1. MACS can save wiggle format files containing the tag number at
	every 10 bp along the genome. Tags are shifted according to our
	model before they are calculated.

	2. Model building and local lambda calculation can be skipped with
	certain options.

	3. A diagnosis report can be generated through '--diag'
	option. This report can help you get an assumption about the
	sequencing saturation. This funtion is only in beta stage.

	4. FDR calculation speed is highly improved.
	
2008-05-28  Tao Liu  <taoliu@jimmy.harvard.edu>
	Version 1.1
	
	* TabIO, PeakModel.py ...
	Bug fixed to let MACS tolerate some cases while there is no tag on
	either plus strand or minus strand.

	* setup.py
	Check the version of python. If the version is lower than 2.4,
	refuse to install with warning.

