def pull_alignments_from(self, reads_to_use, shallow=False):
        """
        Pull out alignments of certain reads

        :param reads_to_use: numpy array of dtype=bool specifying which reads to use
        :param shallow: whether to copy sparse 3D matrix only or not
        :return: a new AlignmentPropertyMatrix object that particular reads are
        """
        new_alnmat = self.copy(shallow=shallow)
        for hid in xrange(self.num_haplotypes):
            hdata = new_alnmat.data[hid]
            hdata.data *= reads_to_use[hdata.indices]
            hdata.eliminate_zeros()
        if new_alnmat.count is not None:
            new_alnmat.count[np.logical_not(reads_to_use)] = 0
        return new_alnmat
def pull_alignments_from(self, reads_to_use, shallow=False):
        """
        Pull out alignments of certain reads

        :param reads_to_use: numpy array of dtype=bool specifying which reads to use
        :param shallow: whether to copy sparse 3D matrix only or not
        :return: a new AlignmentPropertyMatrix object that particular reads are
        """
        new_alnmat = self.copy(shallow=shallow)
        for hid in xrange(self.num_haplotypes):
            hdata = new_alnmat.data[hid]
            hdata.data *= reads_to_use[hdata.indices]
            hdata.eliminate_zeros()
        if new_alnmat.count is not None:
            new_alnmat.count[np.logical_not(reads_to_use)] = 0
        return new_alnmat
def pull_alignments_from ( self , reads_to_use , shallow = False ) : new_alnmat = self . copy ( shallow = shallow ) for hid in xrange ( self . num_haplotypes ) : hdata = new_alnmat . data [ hid ] hdata . data *= reads_to_use [ hdata . indices ] hdata . eliminate_zeros ( ) if new_alnmat . count is not None : new_alnmat . count [ np . logical_not ( reads_to_use ) ] = 0 return new_alnmat
Pull out alignments of certain reads

        :param reads_to_use: numpy array of dtype=bool specifying which reads to use
        :param shallow: whether to copy sparse 3D matrix only or not
        :return: a new AlignmentPropertyMatrix object that particular reads are
Pull out alignments of certain reads : param reads_to_use : numpy array of dtype = bool specifying which reads to use : param shallow : whether to copy sparse 3D matrix only or not : return : a new AlignmentPropertyMatrix object that particular reads are