NAME

       fitgcp - fit mixtures of probability distributions to genome coverage profiles

SYNOPSIS

       fitgcp [options] NAME

DESCRIPTION

       Fits  mixtures  of  probability distributions to genome coverage profiles using an EM-like
       iterative algorithm.

       The script uses a SAM file as input and parses  the  mapping  information  and  creates  a
       Genome  Coverage  Profile  (GCP). The GCP is written to a file, such that this step can be
       skipped the next time.  The user provides a mixture model  that  is  fitted  to  the  GCP.
       Furthermore, the user may specify initial parameters for each model.

       As output, the script generates a text file containing the final set of fit parameters and
       additional information about the fitting process. A log file contains the the current  set
       of  parameters  in  each  step  of  the iteration. If requested, a plot of the GCP and the
       fitted distributions can be created.

OPTIONS

       NAME: Name of SAM file to analyze.

       -h, --help
              show this help message and exit

       -d DIST, --distributions=DIST
              Distributions to fit. z->zero; n: nbinom (MOM); N: nbinom (MLE); p:binom; t:  tail.
              Default: zn

       -i STEPS, --iterations=STEPS
              Maximum number of iterations. Default: 50

       -t THR, --threshold=THR
              Set  the  convergence  threshold  for the iteration. Stop if the change between two
              iterations is less than THR.  Default: 0.01

       -c CUTOFF, --cutoff=CUTOFF
              Specifies a coverage cutoff quantile such that  only  coverage  values  below  this
              quantile are considered.  Default: 0.95

       -p, --plot
              Create a plot of the fitted mixture model. Default: False

       -m MEAN, --means=MEAN
              Specifies  the  initial  values  for  the mean of each Poisson or Negative Binomial
              distribution. Usage: -m 12.4 -m 16.1 will specify  the  means  for  the  first  two
              non-zero/tail distributions. The default is calculated from the data.

       -a ALPHA, --alpha=ALPHA
              Specifies  the initial values for the proportion alpha of each distribution. Usage:
              For three distributions -a 0.3 -a 0.3 specifies the proportions 0.3, 0.3  and  0.4.
              The default is equal proportions for all distributions.

       -l, --log
              Enable logging. Default: False

       --view Only  view  the  GCP.  Do not fit any distribution.  Respects cutoff (-c). Default:
              False