The Platypus variant caller. The main Web site is https://github.com/andyrimmer/Platypus.

To build Platypus, do the following:

    make

Then to run do

    python bin/Platypus.py --bamFiles=BAM.bam --refFile=REF.fa --output=variants.vcf

Platypus has been tested with Python 2.6 and 2.7, and requires Cython 0.20.2 or later to build.

Platypus requires HTSlib 1.2.1 or greater. HTSlib can be downloaded from the HTSlib Web site.

To build and install HTSlib, cd into HTSlib source and type make install. This will install HTSlib under /usr/local/ (see note below). To install HTSlib in any other directory use make install prefix=/path/to/dir.

NOTE: HTSlib should be installed in a standard location (e.g. /usr/local/). If not installed in a standard location, you will need to set your library paths:

• For GNU/Linux:

    export C_INCLUDE_PATH=/path/to/dir/include
    export LIBRARY_PATH=/path/to/dir/lib (only for making)
    export LD_LIBRARY_PATH=/path/to/dir/lib

Note the /include and /lib sub-directories. e.g. if you installed HTSlib under /Users/me/htslib then set

    export C_INCLUDE_PATH=/Users/me/htslib/include
    export LIBRARY_PATH=/Users/me/htslib/lib
    export LD_LIBRARY_PATH=/Users/me/htslib/lib

HTSlib will automatically make the include and lib directories on install.

• For OSX:

    export C_INCLUDE_PATH=/path/to/dir/include
    export LIBRARY_PATH=/path/to/dir/lib (only for making)
    export DYLD_FALLBACK_LIBRARY_PATH=/path/to/dir/lib

To make Platypus compatible with Python 3, the following modifications of Platypus's source code as well as minor tweak in Cython for Python 3.

• Redefine __getslice__ in array.pyx
• Remove __getslice__ check macro of Python 3 in modulenode.py
• Cythonize pyxs in src/pysam to c code
• Update print to print() in main py codes
• Change StandardError to Exception() or raise Exception as
• Update PyString imports in src/pysam/TabProxies.pyx

    from cpython cimport PyErr_SetString, PyBytes_Check, \
    PyUnicode_Check, PyBytes_FromStringAndSize, \
    PyObject_AsFileDescriptor