2023-11-15  Tao Liu  <vladimir.liu@gmail.com>
	MACS 3.0.0

	1) Call variants in peak regions directly from BAM files. The
	function was originally developed under code name SAPPER. Now
	SAPPER has been merged into MACS as the `callvar` command. It can
	be used to call SNVs and small INDELs directly from alignment
	files for ChIP-seq or ATAC-seq. We call `fermi-lite` to assemble
	the DNA sequence at the enriched genomic regions (binding sites or
	accessible DNA) and to refine the alignment when necessary. We
	added `simde` as a submodule in order to support fermi-lite
	library under non-x64 architectures.

	2) HMMRATAC module is added as subcommand `hmmratac`. HMMRATAC is
	a dedicated software to analyze ATAC-seq data. The basic idea
	behind HMMRATAC is to digest ATAC-seq data according to the
	fragment length of read pairs into four signal tracks: short
	fragments, mono-nucleosomal fragments, di-nucleosomal fragments
	and tri-nucleosomal fragments. Then integrate the four tracks
	again using Hidden Markov Model to consider three hidden states:
	open region, nucleosomal region, and background region. The
	orginal paper was published in 2019 written in JAVA, by Evan
	Tarbell. We implemented it in Python/Cython and optimize the whole
	process using existing MACS functions and hmmlearn. Now it can run
	much faster than the original JAVA version. Note: evaluation of
	the peak calling results is still underway.

	3) Speed/memory optimization.  Use the cykhash to replace python
	dictionary. Use buffer (10MB) to read and parse input file (not
	available for BAM file parser). And many optimization tweaks. We
	added memory monitoring to the runtime messages.

	4) R wrappers for MACS -- MACSr for bioconductor.

	5) Code cleanup. Reorganize source codes. 

	6) Unit testing. 

	7) Switch to Github Action for CI, support multi-arch testing
	including x64, armv7, aarch64, s390x and ppc64le. We also test on
	Mac OS 12.

	8) MACS tag-shifting model has been refined. Now it will use a
	naive peak calling approach to find ALL possible paired peaks at +
	and - strand, then use all of them to calculate the
	cross-correlation. (a related bug has been fix
	[#442](https://github.com/macs3-project/MACS/issues/442))

	9) BAI index and random access to BAM file now is
	supported. [#449](https://github.com/macs3-project/MACS/issues/449).

	10) Support of Python > 3.10
	[#498](https://github.com/macs3-project/MACS/issues/498)

	11) The effective genome size parameters have been updated
	according to
	deeptools. [#508](https://github.com/macs3-project/MACS/issues/508)

	12) Multiple updates regarding dependencies, anaconda built, CI/CD
	process.

	13) Cython 3 is supported.

	14) Documentations for each subcommand can be found under /docs

	*Other*

	1) Missing header line while no peaks can be called
	[#501](https://github.com/macs3-project/MACS/issues/501)
	[#502](https://github.com/macs3-project/MACS/issues/502)

	2) Note: different numpy, scipy, sklearn may give slightly
	different results for hmmratac results. The current standard
	results for automated testing in `/test` directory are from Numpy
	1.25.1, Scipy 1.11.1, and sklearn 1.3.0.

2020-04-11  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.2.7.1

	* hotfix:

	Add 'wheel' and 'pip' to pyproject.toml so that `pip install` can
	work.

2020-04-10  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.2.7

	* Bugs fixed

	1) MACS2 has been tested on multiple architectures to make sure it
	can successfully generate consistent results. Currently the
	supported architectures are: AMD64, ARM64, i386, PPC64LE, and
	S390X. Thanks to @mr-c, @junaruga, and @tillea! Related to issue
	#340, #349, #351, and #359; to PR #348, #350, #360, #361, #367,
	and #370. The lesson is that if the project is built on Cython and
	is aimed at memory efficiency, we should specifically define all
	int/float types in pyx files such as int8_t or uint32_t using
	either libc or numpy (c version) instead of relying on Cython
	types such as short, long, double.

	2) MACS2 setup script will check numpy and install numpy if
	necessary. PR #378, issue #364

	3) `bdgbroadcall` command will correctly add the score column (5th
	column). The score (5th) column contains 10 times of the average
	score in the broad region. PR #373, issue #362

	4) The missing test on `bdgopt` subcommand has been added. PR #363

	5) The obsolete option `--ratio` from `callpeak` subcommand has
	been removed. PR #369, issue #366

	6) Fixed the incorrect description in README on the 'maximum
	length of broad region is 4 times of d' to 'maximum gap for
	merging broad regions is 4 times of tag size by default'. PR #380,
	issue #365.

	* Other

	1) CODE OF CONDUCT document has been added to MACS2 github
	repository. PR #358

2019-12-12  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.2.6

	* New Features

	1) Speed up MACS2. Some programming tricks and code cleanup. The
	filter_dup function replaces separate_dups. The later one was
	implemented for potentially putting back duplicate reads in
	certain downstream analysis. However such analysis hasn't been
	implemented. Optimize the speed of writing bedGraph
	files. Optimize BAM and BAMPE parsing with pointer casting instead
	of python unpack.

	2) The comment lines in the headers of BED or SAM files will be
	correctly skipped. However, MACS2 won't check comment lines in the
	middle of the file.

	* Bugs fixed

	1) Cutoff-analysis in callpeak command. #341

	2) Issues related to SAMParser and three ELAND Parsers are
	fixed. #347

	* Other

	1) cmdlinetest script in test/ folder has been updated to: 1. test
	cutoff-analysis with callpeak cmd; 2. output the 2 lines before
	and after the error or warning message during tests; 3. output
	only the first 10 lines if the difference between test result and
	standard result can be found; 4. prockreport monitor CPU time and
	memory usage in 1 sec interval -- a bit more accurate.

	2) Python3.5 support is removed. Now MACS2 requires Python>=3.6.

2019-10-31  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.2.5 (Py3 speed up)

	* Features added

	1) *Github code only and Not included in MACS2 release* New
	testing data for performance test. An subsampled ENCODE2 CTCF
	ChIP-seq dataset, including 5million ChIP reads and 5 million
	control reads, has been included in the test folder for testing
	CPU and memory usage (i.e. 5M test). Several related scripts ,
	including `prockreport` for output cpu memory usage, `pyprofile`
	and `pyprofile_stat` for debuging and profiling MACS2 codes, have
	been included.

	2) Speed up pvalue-qvalue checkup (pqtable checkup) #335 #338.
	The old hashtable.pyx implementation copied from Pandas (very old
	version) doesn't work well in Python3+Cython. It slows down the
	pqtable checkup using the identical Cython codes as in
	v2.1.4. While running 5M test, the `__getitem__` function in the
	hashtable.pyx took 3.5s with 37,382,037 calls in MACS2 v2.1.4, but
	148.6s with the same number of calls in MACS2 v2.2.4. As a
	consequence, the standard python dictionary implementation has
	replaced hashtable.pyx for pqtable checkup. Now MACS2 runs a bit
	faster than py2 version, but uses a bit more memory. In general,
	v2.2.5 can finish 5M reads test in 20% less time than MACS2
	v2.1.4, but use 15% more memory.

	* Bug fixed

	1) More Python3 related fixes, e.g. the return value of keys from
	py3 dict. #333 #337


2019-10-01  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.2.4 (Python3)

	* Features added

	1) First Python3 version MACS2 released.

	2) Version number 2.2.X will be used for MACS2 in Python3, in
	parallel to 2.1.X.

	3) More comprehensive test.sh script to check the consistency of
	results from Python2 version and Python3 version.

	4) Simplify setup.py script since the newest version transparently
	supports cython. And when cython is not installed by the user,
	setup.py can still compile using only C codes.

	5) Fix Signal.pyx to use np.array instead of np.mat.

2019-09-30  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.4

	* Features added

	Github Actions is used together with Travis CI for testing and
	deployment.

	* Bugs fixed

	PR #322:

	1) #318 Random score in bdgdiff output. It turns out the sum_v is
	not initialized as 0 before adding. Potential bugs are fixed in
	other functions in ScoreTrack and CallPeakUnit codes.

	2) #321 Cython dependency in setup.py script is removed. And place
	'cythonzie' call to the correct position.

	3) A typo is fixed in Github Actions script.

2019-09-19  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.3.3

	* Features added

	1) Support Docker auto-deploy. PR #309

	2) Support Travis CI auto-testing, update unit-testing
	scripts, and enable subcommand testing on small datasets.

	3) Update README documents. #297 PR #306

	4) `cmbreps` supports more than 2 replicates. Merged from PR #304
	@Maarten-vd-Sande and PR #307 (our own chi-sq test code)

	5) `--d-min` option is added in `callpeak` and `predictd`, to
	exclude predictions of fragment size smaller than the given
	value. Merged from PR #267 @shouldsee.

	6) `--buffer-size` option is added in `predictd`, `filterdup`,
	`pileup` and `refinepeak` subcommands. Users can use this option
	to decrease memory usage while there are a large number of contigs
	in the data. Also, now `callpeak`, `predictd`, `filterdup`,
	`pileup` and `refinepeak` will suggest users to tweak
	`--buffer-size` while catching a MemoryError. #313 PR #314

	* Bugs fixed

	1) #265 Fixed a bug where the pseudocount hasn't been applied
	while calculating p-value score in ScoreTrack object.

	2) Fixed bdgbroadcall so that it will report those broad peaks
	without strong peak inside, a consistent behavior as `callpeak
	--broad`.

	3) Rename COPYING to LICENSE.

2018-10-17  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.2

	* New features

	1) Added missing BEDPE support. And enable the support for BAMPE
	and BEDPE formats in 'pileup', 'filterdup' and 'randsample'
	subcommands. When format is BAMPE or BEDPE, The 'pileup' command
	will pile up the whole fragment defined by mapping locations of
	the left end and right end of each read pair. Thank @purcaro

	2) Added options to callpeak command for tweaking max-gap and
	min-len during peak calling. Thank @jsh58!

	3) The callpeak option "--to-large" option is replaced with
	"--scale-to large".

	4) The randsample option "-t" has been replaced with "-i".

	* Bug fixes

	1) Fixed memory issue related to #122 and #146

	2) Fixed a bug caused by a typo. Related to #249, Thank @shengqh

	3) Fixed a bug while setting commandline qvalue cutoff.

	4) Better describe the 5th column of narrowPeak. Thank @alexbarrera

	5) Fixed the calculation of average fragment length for paired-end
	data. Thank @jsh58

	6) Fixed bugs caused by khash while computing p/q-value and log
	likelihood ratios. Thank @jsh58

	7) More spelling tweaks in source code. Thank @mr-c

2016-03-09  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.1 20160309

	* Retire the tag:rc.

	* Fixed spelling. Merged pull request #120. Thank @mr-c!

	* Change filtering criteria for reading BAM/SAM files

	Related to callpeak and filterdup commands. Now the
	reads/alignments flagged with 1028 or 'PCR/Optical duplicate' will
	still be read although MACS2 may decide them as duplicates
	later. Related to old issue #33. Sorry I forgot to address it for
	years!

2016-02-26  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.1 20160226 (tag:rc Zhengyue)

	* Bug fixes

	1) Now "-Ofast" has been replaced by "-O3 --ffast-math", because
	the former option is not supported by older GCC. Related to issues
	#91, #109.

	2) Issue #108 is fixed. If no peak can be found in a chromosome,
	the PeakIO won't throw an error.

	* New features

	1) callpeak

	a) A more flexible format, BEDPE, is supported. Now users can
	define the left and right position of the ChIPed fragment, and
	MACS2 will skip model building and directly pileup the
	fragments. Related to issue #112.

	b) The 'tempdir' can be specified, to save cached pileup
	tracks. Originially, the temporary files were stored in
	/tmp. Thank @daler! Related to issues #97 and #105.

	2) bdgopt

	New operations are added, to calculate the maximum or minimum value between
	values in BEDGRAPH and given value.

	3) bdgcmp

	New method is added, to calculate the maximum value between values
	defined in two BEDGRAPH files.

2015-12-22  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.0 20151222 (tag:rc Dongzhi)

	* Bug fixes

	1) Fix a bug while dealing with some chromosomes only containing
	one read (pair). The size of dup_plus/dup_minus arrays after
	filtering dups should +1.

	2) Fix a bug related to the broad peak calling function in
	previous versions. The gaps were miscalculated, so segmented weak
	broad calls may be reported, and sometimes you would see peaks
	with lower than cutoff values in the output files.

	3) "Potentially" Fixed issue #105 on temporary cache files, need
	further followup.


2015-07-31  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.0 20150731 (tag:rc)

	* Bug fixes

	1) Fixed issue #76: information about broad/narrow cutoff will be
	correctly displayed.

	2) Fixed issue #79: bdgopt extparam option is fixed.

	3) Fixed issue #87: reference to cProb has been fixed as 'Prob'
	for filterdup command.

	4) Fixed issue #78, #88 and similar issue reported in MACS google
	group: MACS2 now can correctly deal with multiple alignment files
	for -t or -c. The 'finalize' function will be correctly
	called. Multiple files option is enabled for filterdup,
	randsample, predictd, pileup and refinepeak commands.

	5) A related issue to #88, when BAMPE mode is used, PE pairs will
	be sorted by leftmost then rightmost ends. 

	6) Fixed issue #86: A wrong use of 'ndarray' to create Numpy
	array. This will cause 'callpeak --nolambda' hang forever while
	calculating pvalues and qvalues.

2015-04-20  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.0 20150420 (tag:rc)

	* New commands

	1) bdgopt: some convenient functions to modify bedGraph files.

	2) cmbreps: Combine scores from two replicates. Including three
	methods: 1. take the maximum; 2. take the average; 3. use Fisher's
	method to combine two p-value scores. After that, user can use
	bdgpeakcall to call peaks on combined scores.

	* New features

	1) callpeak and bdgpeakcall now can try to analyze the
	relationship between p-values and number/length of peaks then
	generate a summary to help users decide an appropriate cutoff.

	2) callpeak now can accept fold-enrichment cutoff as a filter for
	final peak calls.

	* Performance

	Now MACS2 runs about 3X as fast as previous version. Trade
	clean python codes for speed... Now while processing 50M ChIP vs
	50M control, it will take only 10 minutes.

	* Bug fixes

	1) Sampling function in BAMPE mode.

	2) Callpeak while there are >= 2 input files for -t or -c.

	3) While reading BAM/SAM, those secondary or supplementary
	alignments will be correctly skipped.

	4) Fixed issue #33: Explanation is added to callpeak --keep-dup
	option that MACS2 will discard those SAM/BAM alignments with bit
	1024 no matter how --keep-dup is set.

	5) Fixed issue #49: setuptools is used intead of distutils

	6) Fixed issue #51: fix the problem when using --trackline
	argument when control file is absent.

	7) Fixed issue #53: Use Use SAM/BAM CIGAR to find the 5' end of
	read mapped to minus strand. Previous implementation will find
	incorrect 5' end if there is indel in alignment.

	8) Fixed issue #56: An incorrect sorting method used for BAMPE
	mode which will cause incorrect filtering of duplicated reads. Now
	fixed.

	9) Issue #63: Merged from jayhesselberth@github, extsize now can
	be 1.

	10) Issue #71: Merged from aertslab@github, close file descriptor
	after creating them with mkstemp().

2014-06-16  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.1.0 20140616 (tag:rc)

	* callpeak module

	"--ratio" is added to manually assign the scaling factor of ChIP
	vs control, e.g. from NCIS. Thank Colin D and Dietmar Rieder for
	implementing the patch file!

	"--shift" is added to move cutting ends (5' end of reads) around,
	in order to process DNAse-Seq data, e.g., use "--shift -100
	--extsize 200" to get 200bps fragments around 5' ends. For general
	ChIP-Seq data analysis, this option should be always set as
	0. Thank Xi Chen and Anshul Kundaje for the discussions in user
	group!

	** Do not output negative fragment size from cross-correlation
	analysis. Thank Alvin Qin for the feedback!

	** --half-ext and --control-shift are removed. For complex read
	shifting and extending, combine '--shift' and '--extsize'
	options. For comparing two conditions, use 'bdgdiff' module
	instead.

	** a bug is fixed to output the last pileup value in bdg file
	correctly.

	* filterdup

	A 'dry-run' option is added to only output numbers, including the
	number of allowed duplicates, the total number of reads before and
	after filtering duplicates and the estimated duplication
	rate. Thank John Urban for the suggestion!


2013-12-16  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20131216 (tag:alpha)

	bug fixes and tweaks

	* We changed license from Artistic License to 3-clauses BSD license.

	Yes. Simpler the better.

	* Process paired-end data with "-f BAMPE" without control

	* GappedPeak output for --broad option has been fixed again to be
	consistent with official UCSC format. We add 1bp pseudo-block to
	left and/or right of broad region when necessary, so that you can
	virtualize the regions without strong enrichment inside
	successfully. In downstream analysis except for virtualization,
	you may need to remove all 1bps blocks from gappedPeak file.

	* diffpeak subcommand is temporarily disabled. Till we
	re-implement it.

2013-10-28  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20131028 (tag:alpha)

	* callpeak --call-summits improvement

	The smoothing window length has been fixed as fragment length
	instead of short read length. The larger smoothing window will
	grant better smoothing results and better sub-peak summits
	detection.

	* --outdir and --ofile options for almost all commands

	Thank Björn Grüning for initially implementing these options!
	Now, MACS2 will save results into a specified
	directory by '--outdir' option, and/or save result into a
	specified file by '--ofile' option. Note, in case '--ofile' is
	available for a subcommand, '-o' now has been adjusted to be the
	same as '--ofile' instead of '--o-prefix'.

	Here is the list of changes. For more detail, use 'macs2 xxx -h'
	for each subcommand:

	** callpeak: --outdir
	** diffpeak: Not implemented
	** bdgpeakcall: --outdir and --ofile
	** bdgbroadcall: --outdir and --ofile
	** bdgcmp: --outdir and --ofile. While --ofile is used, the number
	and the order of arguments for --ofile must be the same as for -m.
	** bdgdiff: --outdir and --ofile
	** filterdup: --outdir
	** pileup: --outdir
	** randsample: --outdir
	** refinepeak: --outdir and --ofile


2013-09-15  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130915 (tag:alpha)

	* callpeak Added a new option --buffer-size

	This option is to tweak a previously hidden parameter that
	controls the steps to increase array size for storing alignment
	information. While in some rare cases, the number of
	chromosomes/contigs/scaffolds is huge, the original default
	setting will cause a huge memory waste. In these cases, we
	recommend to decrease --buffer-size (e.g., 1000) to save memory,
	although the decrease will slow process to read alignment files.

	* an optimization to speed up pvalue-qvalue statistics

	Previously, it took a hour to prepare p-q-table for 65M vs 65M
	human TF library, and now it will take 10 minutes. It was due to a
	single line of code to get a value from a numpy array ...

	* fixed logLR bugs.

2013-07-31  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130731 (tag:alpha)

	* callpeak --call-summits

	Fix bugs causing callpeak --call-summits option generating extra
	number of peaks and inconsistent peak boundaries comparing to
	default option. Thank Ben Levinson!

	* bdgcmp output

	Fix bugs causing bdgcmp output logLR all in positive values. Now
	'depletion' can be correctly represented as negative values.

	* bdgdiff

	Fix the behavior of bdgdiff module. Now it can take four
	bedGraph files, then use logLR as cutoff to call differential
	regions. Check command line of bdgdiff for detail. 

2013-07-13  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130713 (tag:alpha)

	* fix bugs while output broadPeak and gappedPeak.

	Note. Those weak broad regions without any strong enrichment
	regions inside won't be saved in gappedPeak file.

	* bdgcmp -T and -C are merged into -S and description is updated.

	Now, you can use it to override SPMR values in your input for
	bdgcmp. To use SPMR (from 'callpeak --SPMR -B') while calculating
	statistics will cause weird results ( in most cases, lower
	significancy), and won't be consistent with MACS2 callpeak
	behavior. So if you have SPMR bedGraphs, input the smaller/larger
	sample size in MILLION according to 'callpeak --to-large' option.

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.


2013-07-31  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130731 (tag:alpha)

	* callpeak --call-summits

	Fix bugs causing callpeak --call-summits option generating extra
	number of peaks and inconsistent peak boundaries comparing to
	default option. Thank Ben Levinson!

	* bdgcmp output

	Fix bugs causing bdgcmp output logLR all in positive values. Now
	'depletion' can be correctly represented as negative values.

	* bdgdiff

	Fix the behavior of bdgdiff module. Now it can take four
	bedGraph files, then use logLR as cutoff to call differential
	regions. Check command line of bdgdiff for detail. 

2013-07-13  Tao Liu  <vladimir.liu@gmail.com>
	MACS version 2.0.10 20130713 (tag:alpha)

	* fix bugs while output broadPeak and gappedPeak.

	Note. Those weak broad regions without any strong enrichment
	regions inside won't be saved in gappedPeak file.

	* bdgcmp -T and -C are merged into -S and description is updated.

	Now, you can use it to override SPMR values in your input for
	bdgcmp. To use SPMR (from 'callpeak --SPMR -B') while calculating
	statistics will cause weird results ( in most cases, lower
	significancy), and won't be consistent with MACS2 callpeak
	behavior. So if you have SPMR bedGraphs, input the smaller/larger
	sample size in MILLION according to 'callpeak --to-large' option.

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.

