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