Version 1.3.6 (Birthday cake)
"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.
".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.
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)
typo fixed.
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.
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.
Version 1.3.5 (local lambda fixed, typo fixed, model figure improved)
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!
Typo fixed, ELANDParser -> ELANDResultParser
Now, modeled d value will be shown on the model figure.
Version 1.3.4 (Happy New Year Version, bug fixed, ELAND multi/PET support)
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.
Fixed a bug which cause the end positions of every peak region incorrectly added by 1 bp. ( Thanks Mali Salmon!)
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!)
Version 1.3.3 (wiggle bugs fixed)
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, now it's been fixed...
Add an option to save wiggle files on different resolution. (—space)
Version 1.3.2 (tiny bugs fixed)
Fix 65536 -> 65535. ( Thank Joon)
Improved for binomial function with extra large number. Imported from Cistrome project.
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.
Version 1.3.1 (tiny bugs fixed version)
Hyunjin Gene Shin contributed some codes to Prob.py. Now the binomial functions can tolerate large and small numbers.
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.
Version 1.3 (naming clarification version)
'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.
If the redundant tag number at a single position is over 32767, just remember 32767, instead of raising an overflow exception.
fixed a typo.
Bug fixed for diagnosis report.
Version 1.2.2gamma
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. (thanks Bogdan)
Reverse paired peaks in model are rejected. So there will be no negative 'frag_len'. (thanks Bogdan)
Diagnosis function is completed. Which can output a table file for users to estimate their sequencing depth.
Version 1.2
GSL has been totally removed from MACS. Instead, I have implemented the CDF and inverse CDF for poisson and binomial distribution purely in python.
Organize constants used in MACS in the Constants.py file.
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.
Version 1.1
Bug fixed to let MACS tolerate some cases while there is no tag on either plus strand or minus strand.
Check the version of python. If the version is lower than 2.4, refuse to install with warning.
Version 1.0