diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index af6733c..00807f6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,6 +36,5 @@ jobs:
- name: Test granite
run: |
make configure
- make update
make build
make test
diff --git a/docs/API.md b/docs/API.md
index fc5c183..0e1216b 100644
--- a/docs/API.md
+++ b/docs/API.md
@@ -187,7 +187,8 @@ The method *add_values_genotype(ID_genotype, values, sep=':')* allows to add val
vnt_obj.add_values_genotype(ID_genotype, values)
-The method *get_genotype_value(ID_genotype, tag, sep=':')* returns value for tag from the genotype specified by corresponding ID. sep is the tags separator used in format definition and genotype(s).
+The method *get_genotype_value(ID_genotype, tag, complete_genotype=False, sep=':')* returns value for tag from the genotype specified by corresponding ID. sep is the tags separator used in format definition and genotype(s).
+If complete_genotype=True, return '.' if tag is missing. If complete_genotype=False (default) raise exception for the missing tag.
tag_val <str> = vnt_obj.get_genotype_value(ID_genotype, tag)
@@ -207,3 +208,17 @@ The method *get_tag_value(tag, sep=';')* returns the value from tag in INFO. sep
tag_val <str> = vnt_obj.get_tag_value(tag)
*note: tag and ID are case sensitive.*
+
+### Custom error classes
+
+*MissingTag* describes a missing tag or tag value.
+
+*MissingTagDefinition* describes a missing tag definition.
+
+*TagDefinitionError* describes a format error for a tag definition.
+
+*TagFormatError* describes a format error for a tag.
+
+*MissingIdentifier* describes a missing genotype identifier in the VCF file.
+
+*VcfFormatError* describes an error in the VCF format.
diff --git a/docs/conf.py b/docs/conf.py
index 20dccd9..d33fa62 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -22,7 +22,7 @@
author = 'Michele Berselli, Phil Grayson'
# The full version, including alpha/beta/rc tags
-release = '0.2.0'
+release = '0.2.1'
# -- General configuration ---------------------------------------------------
diff --git a/docs/filters.md b/docs/filters.md
index 8b82ed0..430a32f 100644
--- a/docs/filters.md
+++ b/docs/filters.md
@@ -103,6 +103,7 @@ blackList allows to filter-out variants from input VCF file based on positions s
population allele frequency
--afthr AFTHR threshold to filter by population allele frequency
(<=) [1]
+ --BEDfile BEDFILE BED format file with positions to blacklist
```
#### Examples
diff --git a/granite/_version.py b/granite/_version.py
index 90477e9..36509b4 100644
--- a/granite/_version.py
+++ b/granite/_version.py
@@ -1,4 +1,4 @@
"""Version information."""
# The following line *must* be the last in the module, exactly as formatted:
-__version__ = "0.2.0"
+__version__ = "0.2.1"
diff --git a/granite/blackList.py b/granite/blackList.py
index d8217ba..08207e7 100644
--- a/granite/blackList.py
+++ b/granite/blackList.py
@@ -35,8 +35,10 @@ def main(args):
# Variables
afthr, aftag = 0., ''
big_dict = {}
+ BED_bitarrays = {}
is_afthr = True if args['afthr'] else False
is_bigfile = True if args['bigfile'] else False
+ is_BEDfile = True if args['BEDfile'] else False
is_verbose = True if args['verbose'] else False
# Creating Vcf object
@@ -50,9 +52,11 @@ def main(args):
else:
sys.exit('\nERROR in parsing arguments: to filter by population allele frequency please specify the TAG to use\n')
#end if
+ elif is_BEDfile:
+ pass
else:
if not is_bigfile:
- sys.exit('\nERROR in parsing arguments: to blacklist specify a BIG file and/or a threshold for population allele frequency and the TAG to use\n')
+ sys.exit('\nERROR in parsing arguments: to blacklist specify at least a BIG file, a BED file, and/or a threshold for population allele frequency and the TAG to use\n')
#end if
#end if
@@ -63,6 +67,11 @@ def main(args):
if is_bigfile: big_dict = load_big(args['bigfile'])
#end if
+ # BED
+ if is_BEDfile:
+ BED_bitarrays = bed_to_bitarray(args['BEDfile'])
+ #end if
+
# Writing header
vcf_obj.write_header(fo)
@@ -102,6 +111,15 @@ def main(args):
#end if
#end if
+ if is_BEDfile:
+ try: # CHROM and POS can miss in the BED file, if that just pass
+ if BED_bitarrays[vnt_obj.CHROM][vnt_obj.POS]:
+ continue
+ #end if
+ except Exception: pass
+ #end try
+ #end if
+
# All good, pass and write variant
vcf_obj.write_variant(fo, vnt_obj)
#end for
diff --git a/granite/granite.py b/granite/granite.py
index 4d24c3d..6c6dbee 100644
--- a/granite/granite.py
+++ b/granite/granite.py
@@ -103,6 +103,7 @@ def main():
blackList_parser.add_argument('-b', '--bigfile', help='BIG format file with positions set for blacklist', type=str, required=False)
blackList_parser.add_argument('--aftag', help='TAG (TAG=<float>) or TAG field to be used to filter by population allele frequency', type=str, required=False)
blackList_parser.add_argument('--afthr', help='threshold to filter by population allele frequency (<=) [1]', type=float, required=False)
+ blackList_parser.add_argument('--BEDfile', help='BED format file with positions to blacklist', type=str, required=False)
blackList_parser.add_argument('--verbose', help='show progress status in terminal', action='store_true', required=False)
# Add whiteList to subparsers
diff --git a/granite/lib/vcf_parser.py b/granite/lib/vcf_parser.py
index f16251a..f9497e9 100644
--- a/granite/lib/vcf_parser.py
+++ b/granite/lib/vcf_parser.py
@@ -21,6 +21,60 @@
import gzip
+#################################################################
+#
+# Custom errors
+# -> MissingTag
+# -> MissingTagDefinition
+# -> TagDefinitionError
+# -> TagFormatError
+# -> MissingIdentifier
+# -> VcfFormatError
+#
+#################################################################
+class MissingTag(Exception):
+ ''' custom error class,
+ describe a missing tag '''
+
+ def __init__(self, message):
+ self.message = message
+
+class MissingTagDefinition(Exception):
+ ''' custom error class,
+ describe a missing tag definition '''
+
+ def __init__(self, message):
+ self.message = message
+
+class TagDefinitionError(Exception):
+ ''' custom error class,
+ describe a format error for a tag definition '''
+
+ def __init__(self, message):
+ self.message = message
+
+class TagFormatError(Exception):
+ ''' custom error class,
+ describe a format error for a tag '''
+
+ def __init__(self, message):
+ self.message = message
+
+class MissingIdentifier(Exception):
+ ''' custom error class,
+ describe a missing genotype identifier in the VCF'''
+
+ def __init__(self, message):
+ self.message = message
+
+class VcfFormatError(Exception):
+ ''' custom error class,
+ describe a format error in the VCF '''
+
+ def __init__(self, message):
+ self.message = message
+
+
#################################################################
#
# Vcf
@@ -87,7 +141,7 @@ def get_tag_field_idx(self, tag, field, tag_type='INFO', sep='|'):
format = format.replace('\"', '')
format = format.replace('>', '')
except Exception:
- raise ValueError('\nERROR in VCF header structure, {0} tag definition has no format specification\n'
+ raise TagDefinitionError('\nERROR in VCF header structure, {0} tag definition has no format specification\n'
.format(tag))
#end try
# Search exact match
@@ -102,7 +156,7 @@ def get_tag_field_idx(self, tag, field, tag_type='INFO', sep='|'):
#end for
#end if
#end for
- raise ValueError('\nERROR in VCF header structure, {0} tag definition is missing\n'
+ raise MissingTagDefinition('\nERROR in VCF header structure, {0} tag definition is missing\n'
.format(tag))
#end def
@@ -122,7 +176,7 @@ def check_tag_definition(self, tag, tag_type='INFO', sep='|'):
#end if
#end if
#end for
- raise ValueError('\nERROR in VCF header structure, {0} tag definition is missing\n'
+ raise MissingTagDefinition('\nERROR in VCF header structure, {0} tag definition is missing\n'
.format(tag))
#end def
@@ -191,7 +245,7 @@ def remove_tag_genotype(self, tag_to_remove, sep=':'):
#end for
# Error if tag_to_remove not found in FORMAT
if idx_tag_to_remove == -1:
- raise ValueError('\nERROR in variant FORMAT field, {0} tag is missing\n'
+ raise MissingTag('\nERROR in variant FORMAT field, {0} tag is missing\n'
.format(tag_to_remove))
#end if
# Updating FORMAT
@@ -250,7 +304,7 @@ def add_values_genotype(self, ID_genotype, values, sep=':'):
try:
self.GENOTYPES[ID_genotype] += sep + values
except Exception:
- raise ValueError('\nERROR in GENOTYPES identifiers, {0} identifier is missing in VCF\n'
+ raise MissingIdentifier('\nERROR in GENOTYPES identifiers, {0} identifier is missing in VCF\n'
.format(ID_genotype))
#end try
#end def
@@ -272,18 +326,20 @@ def get_tag_value(self, tag_to_get, sep=';'):
try:
return tag.split(tag_to_get + '=')[1]
except Exception: # tag field is in a wrong format
- raise ValueError('\nERROR in variant INFO field, {0} tag is in the wrong format\n'
+ raise TagFormatError('\nERROR in variant INFO field, {0} tag is in the wrong format\n'
.format(tag_to_get))
#end try
#end if
#end for
# tag_to_get not found
- raise ValueError('\nERROR in variant INFO field, {0} tag is missing\n'.format(tag_to_get))
+ raise MissingTag('\nERROR in variant INFO field, {0} tag is missing\n'.format(tag_to_get))
#end def
- def get_genotype_value(self, ID_genotype, tag_to_get, sep=':'):
- ''' get value from tag (tag_to_get) in genotype specified by corresponding ID '''
+ def get_genotype_value(self, ID_genotype, tag_to_get, complete_genotype=False, sep=':'):
+ ''' get value from tag (tag_to_get) in genotype specified by corresponding ID
+ if complete_genotype, return '.' if tag is missing
+ if not complete_genotype, raise Exception for the missing tag '''
# Get index from FORMAT
idx_tag_to_get = -1
for i, tag in enumerate(self.FORMAT.split(sep)):
@@ -294,16 +350,24 @@ def get_genotype_value(self, ID_genotype, tag_to_get, sep=':'):
#end for
# Error if tag_to_get not found in FORMAT
if idx_tag_to_get == -1:
- raise ValueError('\nERROR in variant FORMAT field, {0} tag is missing\n'
+ raise MissingTag('\nERROR in variant FORMAT field, {0} tag is missing\n'
.format(tag_to_get))
#end if
# Get value from index in genotype by ID
- try:
- return self.GENOTYPES[ID_genotype].split(sep)[idx_tag_to_get]
- except Exception:
- raise ValueError('\nERROR in GENOTYPES identifiers, {0} identifier is missing in VCF\n'
+ if self.GENOTYPES.get(ID_genotype):
+ try:
+ return self.GENOTYPES[ID_genotype].split(sep)[idx_tag_to_get]
+ except Exception:
+ if complete_genotype: # expect dropped tags in genotype, return default '.'
+ return '.'
+ else: # expect full genotype, raise error if tag is missing
+ raise MissingTag('\nERROR in variant GENOTYPE field, {0} tag is missing for {1} identifier\n'
+ .format(tag_to_get, ID_genotype))
+ #end try
+ else: # if genotype identifier is missing
+ raise MissingIdentifier('\nERROR in GENOTYPES identifiers, {0} identifier is missing in VCF\n'
.format(ID_genotype))
- #end try
+ #end if
#end def
#end class Variant
@@ -349,7 +413,7 @@ def parse_header(self):
if definitions and columns:
return self.Header(definitions, columns, IDs_genotypes)
else:
- raise ValueError('\nERROR in VCF header structure, missing essential lines\n')
+ raise VcfFormatError('\nERROR in VCF header structure, missing essential lines\n')
#end if
#end def
@@ -362,7 +426,7 @@ def parse_variants(self): # generator
try:
yield self.Variant(line_strip, self.header.IDs_genotypes)
except Exception:
- raise ValueError('\nERROR in variant VCF structure, missing essential columns\n')
+ raise VcfFormatError('\nERROR in variant VCF structure, missing essential columns\n')
#end try
#end if
#end if
diff --git a/poetry.lock b/poetry.lock
index 972e3de..edb3375 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,6 +1,6 @@
[[package]]
name = "atomicwrites"
-version = "1.4.0"
+version = "1.4.1"
description = "Atomic file writes."
category = "dev"
optional = false
@@ -8,21 +8,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "attrs"
-version = "21.4.0"
+version = "22.1.0"
description = "Classes Without Boilerplate"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.5"
[package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
[[package]]
name = "bitarray"
-version = "2.4.1"
+version = "2.6.0"
description = "efficient arrays of booleans -- C extension"
category = "main"
optional = false
@@ -38,7 +38,7 @@ python-versions = "*"
[[package]]
name = "colorama"
-version = "0.4.4"
+version = "0.4.5"
description = "Cross-platform colored terminal text."
category = "dev"
optional = false
@@ -157,8 +157,8 @@ python-versions = ">=3.6"
importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
[package.extras]
-dev = ["pre-commit", "tox"]
-testing = ["pytest", "pytest-benchmark"]
+testing = ["pytest-benchmark", "pytest"]
+dev = ["tox", "pre-commit"]
[[package]]
name = "py"
@@ -181,7 +181,7 @@ diagrams = ["jinja2", "railroad-diagrams"]
[[package]]
name = "pysam"
-version = "0.19.0"
+version = "0.20.0"
description = "pysam"
category = "main"
optional = false
@@ -271,271 +271,33 @@ content-hash = "b6e8b81ee1c0d5e9e28c359042778d40ae84b8d8d4906b3c362d71075722463e
[metadata.files]
atomicwrites = [
- {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
- {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
+ {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
]
attrs = [
- {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
- {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
-]
-bitarray = [
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pluggy = [
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{file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"},
@@ -544,40 +306,10 @@ py = [
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+pysam = []
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python-dateutil = [
{file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
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@@ -586,15 +318,6 @@ six = [
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]
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- {file = "tomli-1.2.3.tar.gz", hash = "sha256:05b6166bff487dc068d322585c7ea4ef78deed501cc124060e0f238e89a9231f"},
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+tomli = []
+typing-extensions = []
+zipp = []
diff --git a/pyproject.toml b/pyproject.toml
index b6b61b2..51943af 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "granite-suite"
-version = "0.2.0"
+version = "0.2.1"
description = "granite is a collection of software to call, filter and work with genomic variants."
authors = ["Michele Berselli <berselli.michele@gmail.com>", "Phil Grayson"]
readme = "README.md"
diff --git a/tests/files/input_BED_blacklist.bed b/tests/files/input_BED_blacklist.bed
new file mode 100644
index 0000000..6ea2e13
--- /dev/null
+++ b/tests/files/input_BED_blacklist.bed
@@ -0,0 +1,5 @@
+track name=pairedReads description="Clone Paired Reads" useScore=1
+1 24152100 24152321
+1 35849464 35849466
+1 20951585 20953585
+3 258099 259199
diff --git a/tests/files/input_blackList_BED.out b/tests/files/input_blackList_BED.out
new file mode 100644
index 0000000..0b96528
--- /dev/null
+++ b/tests/files/input_blackList_BED.out
@@ -0,0 +1,55 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs --output /home/mk446/bio/pipeline/JC50/GENO/1_9874305.comb.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_HG002.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_HG003.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_HG004.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-003.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-011.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-017.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-019.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-024.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-026.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-028.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-033.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-035.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-036.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-052.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-066.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-070.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-088.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-092.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-094.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-106.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-116.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-119.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-120.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-125.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-132.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-133.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-134.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-137.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-141.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-147.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-164.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-165.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-170.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-171.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-172.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-173.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-177.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-181.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-190.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-191.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-193.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-195.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-196.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-197.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-204.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-207.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-208.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-211.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-213.gvcf.gz --variant /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_PSC-01-223.gvcf.gz --reference /home/mk446/BiO/Install/GATK-bundle/2.8/b37/human_g1k_v37_decoy.fasta --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --input-is-somatic false --drop-somatic-filtering-annotations false --ignore-variants-starting-outside-interval false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.2.0",Date="November 18, 2019 11:26:58 AM EST">
+##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output /home/mk446/bio/pipeline/JC50/GENO/1_9874305.geno.vcf.gz --standard-min-confidence-threshold-for-calling 30.0 --dbsnp /home/mk446/BiO/Install/GATK-bundle/dbsnp_147_b37_common_all_20160601.vcf --variant /home/mk446/bio/pipeline/JC50/GENO/1_9874305.comb.gvcf.gz --reference /home/mk446/BiO/Install/GATK-bundle/2.8/b37/human_g1k_v37_decoy.fasta --verbosity INFO --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.2.0",Date="November 18, 2019 11:27:09 AM EST">
+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --dbsnp /home/mk446/BiO/Install/GATK-bundle/dbsnp_147_b37_common_all_20160601.vcf --emit-ref-confidence GVCF --output /home/mk446/bio/pipeline/JC50/GVCF/1_9874305_HG002.gvcf.gz --intervals 1:9874205-9874405 --input /home/mk446/BiO/Data/AshkenazimTrio/b37/HG002.hs37d5.60x/BAM/HG002.hs37d5.60x.1.addrg.bam --reference /home/mk446/BiO/Install/GATK-bundle/2.8/b37/human_g1k_v37_decoy.fasta --verbosity INFO --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --use-filtered-reads-for-annotations false --correct-overlapping-quality false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --consensus false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --max-mnp-distance 0 --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.2.0",Date="November 18, 2019 11:18:23 AM EST">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##source=CombineGVCFs
+##source=GenotypeGVCFs
+##source=HaplotypeCaller
+##MUTANNO=<ID=MUTANNO,Version="0.2",Date="10/29/2019",DataVersion="0.2",DataDate="10/29/2019">
+##MUTANNO=<ID=novoAF,Version="2.1.1",Date="03/06/2019">
+##INFO=<ID=novoAF,Number=.,Type=String,Description="population AF by gnomAD. Format:'AF' ">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002 HG003 HG004 PSC-01-003 PSC-01-011 PSC-01-017
+1 14699 . C G 5732.43 VQSRTrancheSNP99.90to100.00 AC=35;AF=0.350;AN=100;BaseQRankSum=3.04;DP=2321;ExcessHet=46.3686;FS=43.430;InbreedingCoeff=-0.5579;MLEAC=36;MLEAF=0.360;MQ=36.30;MQRankSum=-1.515e+00;QD=3.75;ReadPosRankSum=0.097;SOR=3.624;novoAF=3.41347e-01 GT:AD:DP:GQ:PL 0/1:26,12:38:99:259,0,809 0/0:43,4:47:21:0,21,1381 0/0:26,2:28:43:0,43,902 0/1:97,11:108:16:16,0,2531 0/1:28,4:32:18:18,0,729 0/1:28,15:43:99:338,0,716
+1 66434150 . T C 1279.64 PASS AC=1;AF=0.010;AN=100;BaseQRankSum=2.51;DP=1812;ExcessHet=3.0103;FS=3.005;InbreedingCoeff=-0.0101;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=16.20;ReadPosRankSum=-7.950e-01;SOR=1.009;novoAF=0.0 GT:AD:DP:GQ:PL 0/1:41,38:79:99:1297,0,1309 0/0:63,0:63:99:0,120,1800 0/0:78,0:78:99:0,120,1800 0/0:41,0:41:99:0,106,1456 0/0:34,0:34:90:0,90,1114 0/0:29,0:29:76:0,76,897
+1 168455916 . C T 927.64 PASS AC=1;AF=0.010;AN=100;BaseQRankSum=0.219;DP=1871;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=-0.0101;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=12.71;ReadPosRankSum=0.738;SOR=0.788;novoAF=0.0 GT:AD:DP:GQ:PL 0/1:45,28:73:99:945,0,1606 0/0:63,0:63:99:0,120,1800 0/0:66,0:66:99:0,120,1800 0/0:35,0:35:99:0,99,1485 0/0:34,0:34:99:0,99,1485 0/0:42,0:42:99:0,108,1294
+2 27100779 . T C 1582.64 PASS AC=1;AF=0.010;AN=100;BaseQRankSum=-6.330e-01;DP=1871;ExcessHet=3.0103;FS=17.093;InbreedingCoeff=-0.0101;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=17.58;ReadPosRankSum=1.56;SOR=1.383;novoAF=3.18451e-05 GT:AD:DP:GQ:PL 0/1:43,47:90:99:1600,0,1448 0/0:50,0:50:99:0,120,1800 0/0:67,0:67:99:0,120,1800 0/0:36,0:36:99:0,99,1238 0/0:38,0:38:99:0,111,1665 0/0:37,0:37:99:0,99,1235
+1 26860231 . A T 1082.64 PASS AC=1;AF=0.010;AN=100;BaseQRankSum=1.09;DP=1588;ExcessHet=3.0103;FS=0.985;InbreedingCoeff=-0.0101;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=18.35;ReadPosRankSum=-1.378e+00;SOR=0.853;novoAF=0.324 GT:AD:DP:GQ:PL 0/1:27,32:59:99:1100,0,844 0/0:49,0:49:99:0,120,1800 0/0:49,0:49:99:0,120,1800 0/0:34,0:34:90:0,90,1350 0/0:33,0:33:99:0,99,1080 0/0:37,0:37:99:0,105,1575
+1 23535069 . G GA 606.70 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.010;AN=100;BaseQRankSum=-1.318e+00;DP=1775;ExcessHet=3.8753;FS=14.866;InbreedingCoeff=-0.0466;MLEAC=1;MLEAF=0.010;MQ=68.30;MQRankSum=0.00;QD=9.95;ReadPosRankSum=1.29;SOR=0.723;novoAF=3.46380e-04 GT:AD:DP:GQ:PL 0/1:33,28:61:99:608,0,735 0/0:42,0:42:99:0,104,1458 0/0:66,0:66:99:0,120,1800 0/0:49,0:49:39:0,39,1214 0/0:36,0:36:87:0,87,1082 0/0:36,0:36:99:0,99,1091
+1 15752321 . TCTGA T 857.64 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.010;AN=100;BaseQRankSum=-2.065e+00;DP=1550;ExcessHet=3.0103;FS=13.462;InbreedingCoeff=-0.0101;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=17.87;ReadPosRankSum=1.64;SOR=1.981;novoAF=9.56206e-05 GT:AD:DP:GQ:PL 0/1:25,23:48:99:875,0,1423 0/0:36,0:36:99:0,99,1384 0/0:50,0:50:99:0,120,1800 0/0:34,0:34:99:0,99,1141 0/0:29,0:29:75:0,75,1125 0/0:29,0:29:76:0,76,896
+1 6268385 . A AT 493.68 PASS AC=1;AF=0.010;AN=100;BaseQRankSum=-3.840e-01;DP=1501;ExcessHet=3.0103;FS=2.415;InbreedingCoeff=-0.0102;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=10.29;ReadPosRankSum=-7.640e-01;SOR=0.416;novoAF=3.02251e-03 GT:AD:DP:GQ:PL 0/1:23,25:48:99:511,0,460 0/0:36,0:36:99:0,102,1530 0/0:44,0:44:99:0,105,1686 0/0:27,0:27:75:0,75,1125 0/0:28,0:28:73:0,73,868 0/0:29,0:29:72:0,72,1080
+1 16942782 . G GTATA,GTATATATA,GTATATATATATA,GTATATATATA,GTATATA,GTGTATATATATATATATA 7607.93 PASS AC=3,6,8,9,4,1;AF=0.030,0.060,0.080,0.090,0.040,0.010;AN=100;BaseQRankSum=-1.003e+00;DP=4977;ExcessHet=34.0376;FS=0.648;InbreedingCoeff=-0.4215;MLEAC=3,6,8,9,3,1;MLEAF=0.030,0.060,0.080,0.090,0.030,0.010;MQ=61.24;MQRankSum=0.00;QD=3.18;ReadPosRankSum=0.539;SOR=0.777;novoAF=0.312 GT:AD:DP:GQ:PL 0/1:120,32,0,0,0,0,18:170:99:784,0,7504,1311,7582,8924,1311,7582,8924,8924,1311,7582,8924,8924,8924,1311,7582,8924,8924,8924,8924,512,6153,7505,7505,7505,7505,7646 0/6:157,32,0,0,0,0,26:217:99:1402,452,7812,1794,7966,9586,1794,7966,9586,9586,1794,7966,9586,9586,9586,1794,7966,9586,9586,9586,9586,0,6185,7806,7806,7806,7806,7669 0/0:212,0,0,0,0,0,0:212:99:0,120,1800,120,1800,1800,120,1800,1800,1800,120,1800,1800,1800,1800,120,1800,1800,1800,1800,1800,120,1800,1800,1800,1800,1800,1800 0/2:69,0,8,0,0,0,0:116:65:65,325,3395,0,3070,3117,325,3395,3070,3395,325,3395,3070,3395,3395,325,3395,3070,3395,3395,3395,325,3395,3070,3395,3395,3395,3395 0/2:43,0,12,7,4,0,0:66:99:525,440,2702,0,2199,2155,128,2401,1895,2408,163,2389,1996,2192,2319,440,2702,2199,2401,2389,2702,440,2702,2199,2401,2389,2702,2702 0/0:39,0,0,0,0,0,0:48:99:0,126,2352,126,2352,2352,126,2352,2352,2352,126,2352,2352,2352,2352,126,2352,2352,2352,2352,2352,126,2352,2352,2352,2352,2352,2352
+1 6268385 . A AT 493.68 PASS AC=1;AF=0.010;AN=100;BaseQRankSum=-3.840e-01;DP=1501;ExcessHet=3.0103;FS=2.415;InbreedingCoeff=-0.0102;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=10.29;ReadPosRankSum=-7.640e-01;SOR=0.416;novoAF=3.02251e-03 GT:AD:DP:GQ:PL 0/1:23,25:48:99:511,0,460 0/0:36,0:36:99:0,102,1530 0/0:44,0:44:99:0,105,1686 0/0:27,0:27:75:0,75,1125 0/0:28,0:28:73:0,73,868 0/0:29,0:29:72:0,72,1080
+1 15752321 . TCTGA T 857.64 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.010;AN=100;BaseQRankSum=-2.065e+00;DP=1550;ExcessHet=3.0103;FS=13.462;InbreedingCoeff=-0.0101;MLEAC=1;MLEAF=0.010;MQ=70.00;MQRankSum=0.00;QD=17.87;ReadPosRankSum=1.64;SOR=1.981;novoAF=9.56206e-05 GT:AD:DP:GQ:PL 0/1:25,23:48:99:875,0,1423 0/0:36,0:36:99:0,99,1384 0/0:50,0:50:99:0,120,1800 0/0:34,0:34:99:0,99,1141 0/0:29,0:29:75:0,75,1125 0/0:29,0:29:76:0,76,896
+2 1432699 . C G 5732.43 VQSRTrancheSNP99.90to100.00 AC=35;AF=0.350;AN=100;BaseQRankSum=3.04;DP=2321;ExcessHet=46.3686;FS=43.430;InbreedingCoeff=-0.5579;MLEAC=36;MLEAF=0.360;MQ=36.30;MQRankSum=-1.515e+00;QD=3.75;ReadPosRankSum=0.097;SOR=3.624;novoAF=3.41347e-01 GT:AD:DP:GQ:PL 0/1:26,12:38:99:259,0,809 0/0:43,4:47:21:0,21,1381 0/0:26,2:28:43:0,43,902 0/1:97,11:108:16:16,0,2531 0/1:28,4:32:18:18,0,729 0/1:28,15:43:99:338,0,716
diff --git a/tests/test_SVqcVCF.py b/tests/test_SVqcVCF.py
index 94885c5..2daeeae 100644
--- a/tests/test_SVqcVCF.py
+++ b/tests/test_SVqcVCF.py
@@ -17,14 +17,14 @@ def test_fail_SVqcVCF_no_SVTYPE():
#Variables
args = {'inputfile': 'tests/files/SVqcVCF_no_SVTYPE.vcf.gz','outputfile':'tests/files/main_test.out','samples':["TESTSAMPLE", "TESTSAMPLE2"], 'verbose': None}
# Run and Tests
- with pytest.raises(Exception, match = "ERROR in parsing vcf, variant at position 1:46000 does not contain SVTYPE in INFO"):
+ with pytest.raises(ValueError, match = "ERROR in parsing vcf, variant at position 1:46000 does not contain SVTYPE in INFO"):
main_SVqcVCF(args)
def test_fail_SVqcVCF_wrong_SVTYPE():
#Variables
args = {'inputfile': 'tests/files/SVqcVCF_wrong_SVTYPE.vcf.gz','outputfile':'tests/files/main_test.out','samples':["TESTSAMPLE", "TESTSAMPLE2"], 'verbose': None}
# Run and Tests
- with pytest.raises(Exception, match = "ERROR in parsing vcf, variant at position 1:46000 contains unexpected SVTYPE \"SNV\" in INFO"):
+ with pytest.raises(ValueError, match = "ERROR in parsing vcf, variant at position 1:46000 contains unexpected SVTYPE \"SNV\" in INFO"):
main_SVqcVCF(args)
def test_success_SVqcVCF_twoSamples():
diff --git a/tests/test_blackList.py b/tests/test_blackList.py
index a411ba3..1f97763 100644
--- a/tests/test_blackList.py
+++ b/tests/test_blackList.py
@@ -15,7 +15,7 @@ def test_run_blackList_big():
''' '''
# Variables
args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
- 'aftag': None, 'afthr': None, 'bigfile': 'tests/files/input_blackList.big', 'verbose': None}
+ 'aftag': None, 'afthr': None, 'bigfile': 'tests/files/input_blackList.big', 'BEDfile': None, 'verbose': None}
# Run
main_blackList(args)
# Tests
@@ -28,7 +28,7 @@ def test_run_blackList_032_big():
''' '''
# Variables
args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
- 'aftag': 'novoAF', 'afthr': '0.32', 'bigfile': 'tests/files/input_blackList.big', 'verbose': None}
+ 'aftag': 'novoAF', 'afthr': '0.32', 'bigfile': 'tests/files/input_blackList.big', 'BEDfile': None, 'verbose': None}
# Run
main_blackList(args)
# Tests
@@ -41,7 +41,7 @@ def test_run_blackList_032():
''' '''
# Variables
args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
- 'aftag': 'novoAF', 'afthr': '0.32', 'bigfile': None, 'verbose': None}
+ 'aftag': 'novoAF', 'afthr': '0.32', 'bigfile': None, 'BEDfile': None, 'verbose': None}
# Run
main_blackList(args)
# Tests
@@ -54,7 +54,7 @@ def test_run_blackList_01():
''' '''
# Variables
args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
- 'aftag': 'novoAF', 'afthr': '0.1', 'bigfile': None, 'verbose': None}
+ 'aftag': 'novoAF', 'afthr': '0.1', 'bigfile': None, 'BEDfile': None, 'verbose': None}
# Run
main_blackList(args)
# Tests
@@ -67,7 +67,7 @@ def test_run_blackList_001():
''' '''
# Variables
args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
- 'aftag': 'novoAF', 'afthr': '0.01', 'bigfile': None, 'verbose': None}
+ 'aftag': 'novoAF', 'afthr': '0.01', 'bigfile': None, 'BEDfile': None, 'verbose': None}
# Run
main_blackList(args)
# Tests
@@ -76,6 +76,19 @@ def test_run_blackList_001():
os.remove('tests/files/main_test.out')
#end def
+def test_run_blackList_BED():
+ ''' '''
+ # Variables
+ args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
+ 'aftag': None, 'afthr': None, 'bigfile': None, 'BEDfile': 'tests/files/input_BED_blacklist.bed', 'verbose': None}
+ # Run
+ main_blackList(args)
+ # Tests
+ assert [row for row in open('tests/files/main_test.out')] == [row for row in open('tests/files/input_blackList_BED.out')]
+ # Clean
+ os.remove('tests/files/main_test.out')
+#end def
+
#################################################################
# Errors
@@ -84,18 +97,18 @@ def test_args_afthr_bigfile_missing():
''' '''
# Variables
args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
- 'aftag': None, 'afthr': None, 'bigfile': None, 'verbose': None}
+ 'aftag': None, 'afthr': None, 'bigfile': None, 'BEDfile': None, 'verbose': None}
# Run and Tests
with pytest.raises(SystemExit) as e:
assert main_blackList(args)
- assert str(e.value) == '\nERROR in parsing arguments: to blacklist specify a BIG file and/or a threshold for population allele frequency and the TAG to use\n'
+ assert str(e.value) == '\nERROR in parsing arguments: to blacklist specify at least a BIG file, a BED file, and/or a threshold for population allele frequency and the TAG to use\n'
#end def
def test_args_afthr_conflict():
''' '''
# Variables
args = {'inputfile': 'tests/files/input_blackList.vcf', 'outputfile': 'tests/files/main_test.out',
- 'aftag': None, 'afthr': '0.2', 'bigfile': None, 'verbose': None}
+ 'aftag': None, 'afthr': '0.2', 'bigfile': None, 'BEDfile': None, 'verbose': None}
# Run and Tests
with pytest.raises(SystemExit) as e:
assert main_blackList(args)
@@ -106,7 +119,7 @@ def test_args_afthr_conflict():
# ''' '''
# # Variables
# args = {'inputfile': 'tests/files/input_blackList_novoAF_missing.vcf', 'outputfile': 'tests/files/main_test.out',
-# 'aftag': 'novoAF', 'afthr': '0.2', 'bigfile': None}
+# 'aftag': 'novoAF', 'afthr': '0.2', 'bigfile': None, 'BEDfile': None,}
# # Run and Tests
# with pytest.raises(SystemExit) as e:
# assert main_blackList(args)
diff --git a/tests/test_novoCaller.py b/tests/test_novoCaller.py
index be06b80..75c0083 100644
--- a/tests/test_novoCaller.py
+++ b/tests/test_novoCaller.py
@@ -41,7 +41,7 @@ def assert_(tfile, ofile, test=False):
try:
af_t = float(vnt_obj_t.get_tag_value('novoAF'))
af_o = float(vnt_obj_o.get_tag_value('novoAF'))
- except ValueError:
+ except vcf_parser.MissingTag:
af_t = float(vnt_obj_t.get_tag_value('AlleleFreq'))
af_o = float(vnt_obj_o.get_tag_value('AlleleFreq'))
assert abs(af_t - af_o) < 0.0000000001
@@ -53,7 +53,7 @@ def assert_(tfile, ofile, test=False):
pp_o = float(vnt_obj_o.get_tag_value('novoPP'))
if pp_t > 0.1: assert abs(pp_t - pp_o) < 0.0000000001
else: assert abs(pp_t - pp_o) < 0.0001
- except ValueError as e:
+ except vcf_parser.MissingTag as e:
assert str(e) == '\nERROR in variant INFO field, novoPP tag is missing\n'
# genotypes
for id in vnt_obj_t.IDs_genotypes:
@@ -65,8 +65,8 @@ def assert_(tfile, ofile, test=False):
assert GT_t == GT_o
assert ref_t == ref_o
assert alt_t == alt_o
- except ValueError as e:
- assert str(e) == '\nERROR in GENOTYPES identifiers, PSC-01-003 identifier is missing in VCF\n'
+ except vcf_parser.MissingTag as e:
+ assert str(e) == '\nERROR in variant GENOTYPE field, RSTR tag is missing for PSC-01-003 identifier\n'
#################################################################
# Tests
@@ -470,7 +470,7 @@ def test_run_novoCaller_bam_rerun_noUNR_NORSTR():
'ppthr': None, 'afthr': '0.01', 'aftag': 'novoAF', 'bam': True,
'MQthr': None, 'BQthr': None, 'afthr_unrelated': 0.01, 'ADthr': 3, 'verbose': None}
# Run and Tests
- with pytest.raises(ValueError) as e:
+ with pytest.raises(vcf_parser.MissingTag) as e:
assert main_novoCaller(args)
assert '\nERROR in variant FORMAT field, RSTR tag is missing\n' == str(e.value)
# Clean
diff --git a/tests/test_toBig.py b/tests/test_toBig.py
index 9b64098..b13fa3e 100644
--- a/tests/test_toBig.py
+++ b/tests/test_toBig.py
@@ -378,7 +378,7 @@ def test_run_toBig_rdthr_2_all_miss_pos():
'regionfile': 'tests/files/input_toBig.regions',
'chromfile': 'tests/files/input_toBig.chrom.size'}
# Run and Tests
- with pytest.raises(Exception) as e:
+ with pytest.raises(IndexError) as e:
assert main_toBig(args)
assert str(e.value) == '\nERROR in file: position 13:11006 in file tests/files/input_toBig_miss_pos.rck.gz is not consistent with other files\n'
#end def