New in MACS 1.4.0 ( between MACS 1.3.7.1 )

* Model building: The default behavior in the model building step is
  changed. When MACS can't find enough pairs to build model 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 behavior.

* Redundant tag filtering: MACS now can allow multiple reads at the
  same position. 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. 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.

* Scaling between channels: --to-small. Default behavior is to always
  scale smaller datasets ( ChIP or control ) towards the bigger
  one. When --to-small is on, bigger dataset will be scaled down
  towards smaller one.

* Peak summits and subpeaks: An extra summit position output
  NAME_summits.bed is provided. An option '--call-subpeaks' will
  invoke PeakSplitter developed by Mali Salmon to split wide peaks
  into smaller subpeaks.

* Automatically detect tag size. However to specify the correct tag
  size can avoid unexpected mistakes.

* Sniff -- automatic format detection on input files. However to
  specify the correct file format can avoid unexpected mistakes.

* Short names for effective genome size option, for human, mouse,
  C. elegans and fruitfly.

* Local lambda regions. --lambdaset is replaced by --slocal and
  --llocal which mean the small local region and large local
  region. MACS will check peak_region, slocal( default 1K) and llocal
  (default 10K) for the local bias.

* --bw has no effect on the scan-window size now. It only affects the
    paired-peaks model process.
	
* elandexport2bed.py, elandmulti2bed.py, elandresult2bed.py,
  sam2bed.py extension '.py' are all removed, so the commands are
  elandexport2bed, elandmulti2bed, elandresult2bed and sam2bed.

* Single wiggle file or bedGraph file output

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

* Post-process script for a combined wig file with -10log10pvalue
  scores.

* And tons of bugs are fixed.
