#! python
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"""This script defines BamPostService, which
   * calls 'samtools sort' to sort out.bam, and
   * calls 'samtools index' to make out.bai index, and
   * calls 'makePbi.py' to make out.pbi index file.
"""

# Author: Yuan Li

from __future__ import absolute_import
import logging
from pbalign.service import Service
from pbalign.utils.progutil import Execute


class BamPostService(Service):

    """Sort a bam, makes bam index and PacBio index."""
    @property
    def name(self):
        """Name of bam post service."""
        return "BamPostService"

    @property
    def progName(self):
        return "samtools"

    @property
    def cmd(self):
        return ""

    def __init__(self, filenames):
        """Initialize a BamPostService object.
            Input - unsortedBamFile: a filtered, unsorted bam file
                    refFasta : a reference fasta file
            Output - sortedBamFile: sorted BAM file
                     outBaiFile: index BAI file
        """
        self.refFasta = filenames.targetFileName

        # filtered, unsorted bam file.
        self.unsortedBamFile = filenames.filteredSam
        self.outBamFile = filenames.outBamFileName
        self.outBaiFile = filenames.outBaiFileName
        self.outPbiFile = filenames.outPbiFileName

    def _sortbam(self, unsortedBamFile, sortedBamFile):
        """Sort unsortedBamFile and output sortedBamFile."""
        if not sortedBamFile.endswith(".bam"):
            raise ValueError("sorted bam file name %s must end with .bam" %
                             sortedBamFile)
        sortedPrefix = sortedBamFile[0:-4]
        cmd = 'samtools --version'
        _samtoolsversion = ["0","1","19"]
        try:
            _out, _code, _msg = Execute(self.name, cmd)
            if "samtools" in _out[0]:
                _samtoolsversion = str(_out[0][8:]).strip().split('.')
            else:
                pass
        except Exception:
            pass
        _stvmajor = int(_samtoolsversion[0])
        if _stvmajor >= 1:
            cmd = 'samtools sort -m 4G -o {sortedBamFile} {unsortedBamFile}'.format(
                sortedBamFile=sortedBamFile, unsortedBamFile=unsortedBamFile)
        else:
            cmd = 'samtools sort -m 4G {unsortedBamFile} {prefix}'.format(
                unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)
        Execute(self.name, cmd)

    def _makebai(self, sortedBamFile, outBaiFile):
        """Build *.bai index file."""
        cmd = 'samtools --version'
        _samtoolsversion = ["0","1","19"]
        try:
            _out, _code, _msg = Execute(self.name, cmd)
            if "samtools" in _out[0]:
                _samtoolsversion = str(_out[0][8:]).strip().split('.')
            else:
                pass
        except Exception:
            pass
        _stvmajor = int(_samtoolsversion[0])
        _stvminor = int(_samtoolsversion[1])
        if _stvmajor == 1 and _stvminor == 2:
            # only for 1.2
            cmd = "samtools index {sortedBamFile}".format(
                sortedBamFile=sortedBamFile)
        else:
            cmd = "samtools index {sortedBamFile} {outBaiFile}".format(
                sortedBamFile=sortedBamFile, outBaiFile=outBaiFile)
        Execute(self.name, cmd)

    def _makepbi(self, sortedBamFile):
        """Generate *.pbi PacBio BAM index."""
        cmd = "pbindex %s" % sortedBamFile
        Execute(self.name, cmd)

    def run(self):
        """ Run the BAM post-processing service. """
        logging.info(self.name + ": Sort and build index for a bam file.")
        self._sortbam(unsortedBamFile=self.unsortedBamFile,
                      sortedBamFile=self.outBamFile)
        self._makebai(sortedBamFile=self.outBamFile,
                      outBaiFile=self.outBaiFile)
        self._makepbi(sortedBamFile=self.outBamFile)
