from ConfigParser import SafeConfigParser

### global variables ###
configReader = SafeConfigParser()
project_name = ''
infile = ''
cnv_bed = ''
cnv_list_dir = ''
cancer_type = ''
spltbams_path = ''
het_path = ''
nonhet_path = ''
outbamfn = ''
results_path = ''
java_path = ''
beagle_path = ''
picard_path = ''
samtools_path = ''
bedtools_path = ''
vcftools_path = ''
phase = False
ctDNA = False
singleXY = False


def InitConfigReader(configFile):
    """init the config file"""
    configReader.readfp(open(configFile))


def GetConfigReader():
    """return the configreader"""
    return configReader

def GetVCFPath():
    return vcf_path

def SetVCFPath(path):
    global vcf_path
    vcf_path = path

def GetExonsPath():
    return exons_path

def SetExonsPath(path):
    global exons_path
    exons_path = path

def GetResultsPath():
    return results_path

def SetResultsPath(path):
    global results_path
    results_path = path


def GetSplitBamsPath():
    return spltbams_path


def SetSplitBamsPath(spltbams):
    global spltbams_path
    spltbams_path = spltbams


def SetCancerType(can_type):
    global cancer_type
    cancer_type = can_type


def GetCancerType():
    return cancer_type


def SetOutputFileName(out_bam_file):
    global outbamfn
    outbamfn = out_bam_file


def GetOutputFileName():
    return outbamfn


def SetLogPath(path):
    global log_path
    log_path = path


def GetLogPath():
    return log_path


def SetHetPath(path):
    global het_path
    het_path = path


def GetHetPath():
    return het_path


def SetNonHetPath(path):
    global nonhet_path
    nonhet_path = path


def GetNonHetPath():
    return nonhet_path


def SetJavaPath(path):
    global java_path
    java_path = path


def GetJavaPath():
    return java_path


def SetBeaglePath(path):
    global java_path
    java_path = path

def GetBeaglePath():
    return java_path

def SetPicardPath(path):
    global java_path
    java_path = path

def GetPicardPath():
    return java_path

def SetCNV(cnv):
    global cnv_bed
    cnv_bed = cnv


def GetCNV():
    return cnv_bed


def SetCNVDir(cnv_l):
    global cnv_list_dir
    cnv_list_dir = cnv_l


def GetCNVDir():
    return cnv_list_dir


def SetPhase(Phase):
    global phase
    phase = Phase


def GetPhase():
    return phase


def GetctDNA():
    return ctDNA


def SetctDNA(ctdna):
    global ctDNA
    ctDNA = ctdna


def GetXY():
    return singleXY


def SetXY(xy):
    global singleXY
    singleXY = xy


def SetSoftwarePath(j_path, b_path, p_path, s_path, bd_path, v_path, sb_path):
    configReader.set('SOFTWARE', 'java_path', str(j_path))
    configReader.set('SOFTWARE', 'beagle_path', str(b_path))
    configReader.set('SOFTWARE', 'picard_path', str(p_path))
    configReader.set('SOFTWARE', 'samtools_path', str(s_path))
    configReader.set('SOFTWARE', 'bedtools_path', str(bd_path))
    configReader.set('SOFTWARE', 'vcftools_path', str(v_path))
    configReader.set('SOFTWARE', 'sambamba_path', str(sb_path))


def GetSoftwarePath():
    java_path = configReader.get('SOFTWARE', 'java_path')
    beagle_path = configReader.get('SOFTWARE', 'beagle_path')
    picard_path = configReader.get('SOFTWARE', 'picard_path')
    samtools_path = configReader.get('SOFTWARE', 'samtools_path')
    bedtools_path = configReader.get('SOFTWARE', 'bedtools_path')
    vcftools_path = configReader.get('SOFTWARE', 'vcftools_path')
    sambamba_path = configReader.get('SOFTWARE', 'sambamba_path')

    return java_path, beagle_path, picard_path, samtools_path, bedtools_path, vcftools_path, sambamba_path

a96633a5d0aa9bc678af943618f1d8cddf490fbc
<mask token>


def SetVCFPath(path):
    global vcf_path
    vcf_path = path


def GetExonsPath():
    return exons_path


<mask token>


def SetResultsPath(path):
    global results_path
    results_path = path


def GetSplitBamsPath():
    return spltbams_path


def SetSplitBamsPath(spltbams):
    global spltbams_path
    spltbams_path = spltbams


<mask token>


def GetCancerType():
    return cancer_type


def SetOutputFileName(out_bam_file):
    global outbamfn
    outbamfn = out_bam_file


def GetOutputFileName():
    return outbamfn


<mask token>


def GetLogPath():
    return log_path


<mask token>


def GetHetPath():
    return het_path


def SetNonHetPath(path):
    global nonhet_path
    nonhet_path = path


def GetNonHetPath():
    return nonhet_path


<mask token>


def GetBeaglePath():
    return java_path


def SetPicardPath(path):
    global java_path
    java_path = path


def GetPicardPath():
    return java_path


<mask token>


def SetCNVDir(cnv_l):
    global cnv_list_dir
    cnv_list_dir = cnv_l


<mask token>


def GetctDNA():
    return ctDNA


def SetctDNA(ctdna):
    global ctDNA
    ctDNA = ctdna


<mask token>

<mask token>


def InitConfigReader(configFile):
    """init the config file"""
    configReader.readfp(open(configFile))


def GetConfigReader():
    """return the configreader"""
    return configReader


def GetVCFPath():
    return vcf_path


def SetVCFPath(path):
    global vcf_path
    vcf_path = path


def GetExonsPath():
    return exons_path


def SetExonsPath(path):
    global exons_path
    exons_path = path


def GetResultsPath():
    return results_path


def SetResultsPath(path):
    global results_path
    results_path = path


def GetSplitBamsPath():
    return spltbams_path


def SetSplitBamsPath(spltbams):
    global spltbams_path
    spltbams_path = spltbams


<mask token>


def GetCancerType():
    return cancer_type


def SetOutputFileName(out_bam_file):
    global outbamfn
    outbamfn = out_bam_file


def GetOutputFileName():
    return outbamfn


def SetLogPath(path):
    global log_path
    log_path = path


def GetLogPath():
    return log_path


def SetHetPath(path):
    global het_path
    het_path = path


def GetHetPath():
    return het_path


def SetNonHetPath(path):
    global nonhet_path
    nonhet_path = path


def GetNonHetPath():
    return nonhet_path


def SetJavaPath(path):
    global java_path
    java_path = path


<mask token>


def GetBeaglePath():
    return java_path


def SetPicardPath(path):
    global java_path
    java_path = path


def GetPicardPath():
    return java_path


def SetCNV(cnv):
    global cnv_bed
    cnv_bed = cnv


def GetCNV():
    return cnv_bed


def SetCNVDir(cnv_l):
    global cnv_list_dir
    cnv_list_dir = cnv_l


def GetCNVDir():
    return cnv_list_dir


<mask token>


def GetctDNA():
    return ctDNA


def SetctDNA(ctdna):
    global ctDNA
    ctDNA = ctdna


<mask token>


def SetXY(xy):
    global singleXY
    singleXY = xy


<mask token>


def GetSoftwarePath():
    java_path = configReader.get('SOFTWARE', 'java_path')
    beagle_path = configReader.get('SOFTWARE', 'beagle_path')
    picard_path = configReader.get('SOFTWARE', 'picard_path')
    samtools_path = configReader.get('SOFTWARE', 'samtools_path')
    bedtools_path = configReader.get('SOFTWARE', 'bedtools_path')
    vcftools_path = configReader.get('SOFTWARE', 'vcftools_path')
    sambamba_path = configReader.get('SOFTWARE', 'sambamba_path')
    return (java_path, beagle_path, picard_path, samtools_path,
        bedtools_path, vcftools_path, sambamba_path)

<mask token>


def InitConfigReader(configFile):
    """init the config file"""
    configReader.readfp(open(configFile))


def GetConfigReader():
    """return the configreader"""
    return configReader


def GetVCFPath():
    return vcf_path


def SetVCFPath(path):
    global vcf_path
    vcf_path = path


def GetExonsPath():
    return exons_path


def SetExonsPath(path):
    global exons_path
    exons_path = path


def GetResultsPath():
    return results_path


def SetResultsPath(path):
    global results_path
    results_path = path


def GetSplitBamsPath():
    return spltbams_path


def SetSplitBamsPath(spltbams):
    global spltbams_path
    spltbams_path = spltbams


def SetCancerType(can_type):
    global cancer_type
    cancer_type = can_type


def GetCancerType():
    return cancer_type


def SetOutputFileName(out_bam_file):
    global outbamfn
    outbamfn = out_bam_file


def GetOutputFileName():
    return outbamfn


def SetLogPath(path):
    global log_path
    log_path = path


def GetLogPath():
    return log_path


def SetHetPath(path):
    global het_path
    het_path = path


def GetHetPath():
    return het_path


def SetNonHetPath(path):
    global nonhet_path
    nonhet_path = path


def GetNonHetPath():
    return nonhet_path


def SetJavaPath(path):
    global java_path
    java_path = path


def GetJavaPath():
    return java_path


def SetBeaglePath(path):
    global java_path
    java_path = path


def GetBeaglePath():
    return java_path


def SetPicardPath(path):
    global java_path
    java_path = path


def GetPicardPath():
    return java_path


def SetCNV(cnv):
    global cnv_bed
    cnv_bed = cnv


def GetCNV():
    return cnv_bed


def SetCNVDir(cnv_l):
    global cnv_list_dir
    cnv_list_dir = cnv_l


def GetCNVDir():
    return cnv_list_dir


<mask token>


def GetPhase():
    return phase


def GetctDNA():
    return ctDNA


def SetctDNA(ctdna):
    global ctDNA
    ctDNA = ctdna


<mask token>


def SetXY(xy):
    global singleXY
    singleXY = xy


def SetSoftwarePath(j_path, b_path, p_path, s_path, bd_path, v_path, sb_path):
    configReader.set('SOFTWARE', 'java_path', str(j_path))
    configReader.set('SOFTWARE', 'beagle_path', str(b_path))
    configReader.set('SOFTWARE', 'picard_path', str(p_path))
    configReader.set('SOFTWARE', 'samtools_path', str(s_path))
    configReader.set('SOFTWARE', 'bedtools_path', str(bd_path))
    configReader.set('SOFTWARE', 'vcftools_path', str(v_path))
    configReader.set('SOFTWARE', 'sambamba_path', str(sb_path))


def GetSoftwarePath():
    java_path = configReader.get('SOFTWARE', 'java_path')
    beagle_path = configReader.get('SOFTWARE', 'beagle_path')
    picard_path = configReader.get('SOFTWARE', 'picard_path')
    samtools_path = configReader.get('SOFTWARE', 'samtools_path')
    bedtools_path = configReader.get('SOFTWARE', 'bedtools_path')
    vcftools_path = configReader.get('SOFTWARE', 'vcftools_path')
    sambamba_path = configReader.get('SOFTWARE', 'sambamba_path')
    return (java_path, beagle_path, picard_path, samtools_path,
        bedtools_path, vcftools_path, sambamba_path)

from ConfigParser import SafeConfigParser
configReader = SafeConfigParser()
project_name = ''
infile = ''
cnv_bed = ''
cnv_list_dir = ''
cancer_type = ''
spltbams_path = ''
het_path = ''
nonhet_path = ''
outbamfn = ''
results_path = ''
java_path = ''
beagle_path = ''
picard_path = ''
samtools_path = ''
bedtools_path = ''
vcftools_path = ''
phase = False
ctDNA = False
singleXY = False


def InitConfigReader(configFile):
    """init the config file"""
    configReader.readfp(open(configFile))


def GetConfigReader():
    """return the configreader"""
    return configReader


def GetVCFPath():
    return vcf_path


def SetVCFPath(path):
    global vcf_path
    vcf_path = path


def GetExonsPath():
    return exons_path


def SetExonsPath(path):
    global exons_path
    exons_path = path


def GetResultsPath():
    return results_path


def SetResultsPath(path):
    global results_path
    results_path = path


def GetSplitBamsPath():
    return spltbams_path


def SetSplitBamsPath(spltbams):
    global spltbams_path
    spltbams_path = spltbams


def SetCancerType(can_type):
    global cancer_type
    cancer_type = can_type


def GetCancerType():
    return cancer_type


def SetOutputFileName(out_bam_file):
    global outbamfn
    outbamfn = out_bam_file


def GetOutputFileName():
    return outbamfn


def SetLogPath(path):
    global log_path
    log_path = path


def GetLogPath():
    return log_path


def SetHetPath(path):
    global het_path
    het_path = path


def GetHetPath():
    return het_path


def SetNonHetPath(path):
    global nonhet_path
    nonhet_path = path


def GetNonHetPath():
    return nonhet_path


def SetJavaPath(path):
    global java_path
    java_path = path


def GetJavaPath():
    return java_path


def SetBeaglePath(path):
    global java_path
    java_path = path


def GetBeaglePath():
    return java_path


def SetPicardPath(path):
    global java_path
    java_path = path


def GetPicardPath():
    return java_path


def SetCNV(cnv):
    global cnv_bed
    cnv_bed = cnv


def GetCNV():
    return cnv_bed


def SetCNVDir(cnv_l):
    global cnv_list_dir
    cnv_list_dir = cnv_l


def GetCNVDir():
    return cnv_list_dir


def SetPhase(Phase):
    global phase
    phase = Phase


def GetPhase():
    return phase


def GetctDNA():
    return ctDNA


def SetctDNA(ctdna):
    global ctDNA
    ctDNA = ctdna


def GetXY():
    return singleXY


def SetXY(xy):
    global singleXY
    singleXY = xy


def SetSoftwarePath(j_path, b_path, p_path, s_path, bd_path, v_path, sb_path):
    configReader.set('SOFTWARE', 'java_path', str(j_path))
    configReader.set('SOFTWARE', 'beagle_path', str(b_path))
    configReader.set('SOFTWARE', 'picard_path', str(p_path))
    configReader.set('SOFTWARE', 'samtools_path', str(s_path))
    configReader.set('SOFTWARE', 'bedtools_path', str(bd_path))
    configReader.set('SOFTWARE', 'vcftools_path', str(v_path))
    configReader.set('SOFTWARE', 'sambamba_path', str(sb_path))


def GetSoftwarePath():
    java_path = configReader.get('SOFTWARE', 'java_path')
    beagle_path = configReader.get('SOFTWARE', 'beagle_path')
    picard_path = configReader.get('SOFTWARE', 'picard_path')
    samtools_path = configReader.get('SOFTWARE', 'samtools_path')
    bedtools_path = configReader.get('SOFTWARE', 'bedtools_path')
    vcftools_path = configReader.get('SOFTWARE', 'vcftools_path')
    sambamba_path = configReader.get('SOFTWARE', 'sambamba_path')
    return (java_path, beagle_path, picard_path, samtools_path,
        bedtools_path, vcftools_path, sambamba_path)

from ConfigParser import SafeConfigParser

### global variables ###
configReader = SafeConfigParser()
project_name = ''
infile = ''
cnv_bed = ''
cnv_list_dir = ''
cancer_type = ''
spltbams_path = ''
het_path = ''
nonhet_path = ''
outbamfn = ''
results_path = ''
java_path = ''
beagle_path = ''
picard_path = ''
samtools_path = ''
bedtools_path = ''
vcftools_path = ''
phase = False
ctDNA = False
singleXY = False


def InitConfigReader(configFile):
    """init the config file"""
    configReader.readfp(open(configFile))


def GetConfigReader():
    """return the configreader"""
    return configReader

def GetVCFPath():
    return vcf_path

def SetVCFPath(path):
    global vcf_path
    vcf_path = path

def GetExonsPath():
    return exons_path

def SetExonsPath(path):
    global exons_path
    exons_path = path

def GetResultsPath():
    return results_path

def SetResultsPath(path):
    global results_path
    results_path = path


def GetSplitBamsPath():
    return spltbams_path


def SetSplitBamsPath(spltbams):
    global spltbams_path
    spltbams_path = spltbams


def SetCancerType(can_type):
    global cancer_type
    cancer_type = can_type


def GetCancerType():
    return cancer_type


def SetOutputFileName(out_bam_file):
    global outbamfn
    outbamfn = out_bam_file


def GetOutputFileName():
    return outbamfn


def SetLogPath(path):
    global log_path
    log_path = path


def GetLogPath():
    return log_path


def SetHetPath(path):
    global het_path
    het_path = path


def GetHetPath():
    return het_path


def SetNonHetPath(path):
    global nonhet_path
    nonhet_path = path


def GetNonHetPath():
    return nonhet_path


def SetJavaPath(path):
    global java_path
    java_path = path


def GetJavaPath():
    return java_path


def SetBeaglePath(path):
    global java_path
    java_path = path

def GetBeaglePath():
    return java_path

def SetPicardPath(path):
    global java_path
    java_path = path

def GetPicardPath():
    return java_path

def SetCNV(cnv):
    global cnv_bed
    cnv_bed = cnv


def GetCNV():
    return cnv_bed


def SetCNVDir(cnv_l):
    global cnv_list_dir
    cnv_list_dir = cnv_l


def GetCNVDir():
    return cnv_list_dir


def SetPhase(Phase):
    global phase
    phase = Phase


def GetPhase():
    return phase


def GetctDNA():
    return ctDNA


def SetctDNA(ctdna):
    global ctDNA
    ctDNA = ctdna


def GetXY():
    return singleXY


def SetXY(xy):
    global singleXY
    singleXY = xy


def SetSoftwarePath(j_path, b_path, p_path, s_path, bd_path, v_path, sb_path):
    configReader.set('SOFTWARE', 'java_path', str(j_path))
    configReader.set('SOFTWARE', 'beagle_path', str(b_path))
    configReader.set('SOFTWARE', 'picard_path', str(p_path))
    configReader.set('SOFTWARE', 'samtools_path', str(s_path))
    configReader.set('SOFTWARE', 'bedtools_path', str(bd_path))
    configReader.set('SOFTWARE', 'vcftools_path', str(v_path))
    configReader.set('SOFTWARE', 'sambamba_path', str(sb_path))


def GetSoftwarePath():
    java_path = configReader.get('SOFTWARE', 'java_path')
    beagle_path = configReader.get('SOFTWARE', 'beagle_path')
    picard_path = configReader.get('SOFTWARE', 'picard_path')
    samtools_path = configReader.get('SOFTWARE', 'samtools_path')
    bedtools_path = configReader.get('SOFTWARE', 'bedtools_path')
    vcftools_path = configReader.get('SOFTWARE', 'vcftools_path')
    sambamba_path = configReader.get('SOFTWARE', 'sambamba_path')

    return java_path, beagle_path, picard_path, samtools_path, bedtools_path, vcftools_path, sambamba_path
