hapsburg.PackagesSupport.loadEigenstrat.saveHDF5
================================================

.. py:module:: hapsburg.PackagesSupport.loadEigenstrat.saveHDF5

.. autoapi-nested-parse::

   Functions to save hdf5, and transfrom Eigenstrat to hdf5
   @ Author: Harald Ringbauer, 2019, All rights reserved



Functions
---------

.. autoapisummary::

   hapsburg.PackagesSupport.loadEigenstrat.saveHDF5.save_hdf5
   hapsburg.PackagesSupport.loadEigenstrat.saveHDF5.eigenstrat_to_hdf5
   hapsburg.PackagesSupport.loadEigenstrat.saveHDF5.mpileup2hdf5
   hapsburg.PackagesSupport.loadEigenstrat.saveHDF5.bam2hdf5
   hapsburg.PackagesSupport.loadEigenstrat.saveHDF5.mpileup2hdf5_damageAware
   hapsburg.PackagesSupport.loadEigenstrat.saveHDF5.bamTable2hdf5


Module Contents
---------------

.. py:function:: save_hdf5(path, gt, ref, alt, pos, chs, rec, samples, ad=[], sex=[], clst=[], compression='gzip', gt_type='int8')

   Create a new HDF5 File with Input Data.
   Field Names are chosen to integrate with hapROH
   gt: Genotype data [l,k,2]
   ad: Allele depth [l,k,2]
   ref: Reference Allele [l]
   alt: Alternate Allele [l]
   pos: Position  [l]
   chs: Chromosome [l]
   m: Map position [l]
   samples: Sample IDs [k].
   Save genotype data as int8, readcount data as int16.
   ad: whether to save allele depth
   gt_type: What genotype data type save.
   sex: Vector of Sex [k]
   clst: Vector of Cluster [k]


.. py:function:: eigenstrat_to_hdf5(path_es='', path_hdf5='', packed=True, sep='\\s+')

   Translates eigenstrat to hdf5 file. Saves new file.
   path_es: Path of the Eigenstrat [string]
   path_hdf5: Path of the hdf5 [string]


.. py:function:: mpileup2hdf5(path2mpileup, refHDF5, iid='', s=-np.inf, e=np.inf, outPath='', output=True, maxdepth=127)

.. py:function:: bam2hdf5(path2bam, refHDF5, ch='X', iid='', minMapQual=30, minBaseQual=20, s=-np.inf, e=np.inf, trim=0, outPath='', output=True)

.. py:function:: mpileup2hdf5_damageAware(path2mpileup, refHDF5, iid='', s=-np.inf, e=np.inf, outPath='', output=True)

.. py:function:: bamTable2hdf5(path2bamTable, refHDF5, iid='', s=-np.inf, e=np.inf, outPath='', output=True)