GPatch 0.3.4__tar.gz → 0.3.5__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {GPatch-0.3.4/src/GPatch.egg-info → GPatch-0.3.5}/PKG-INFO +1 -1
- {GPatch-0.3.4 → GPatch-0.3.5}/setup.py +1 -1
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch/GPatch.py +3 -3
- {GPatch-0.3.4 → GPatch-0.3.5/src/GPatch.egg-info}/PKG-INFO +1 -1
- {GPatch-0.3.4 → GPatch-0.3.5}/CODE_OF_CONDUCT.md +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/LICENSE +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/MANIFEST.in +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/README.md +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/pyproject.toml +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/requirements.txt +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/setup.cfg +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch/__init__.py +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch/__main__.py +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch.egg-info/SOURCES.txt +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch.egg-info/dependency_links.txt +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch.egg-info/entry_points.txt +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch.egg-info/not-zip-safe +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch.egg-info/requires.txt +0 -0
- {GPatch-0.3.4 → GPatch-0.3.5}/src/GPatch.egg-info/top_level.txt +0 -0
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@@ -29,7 +29,7 @@ def main():
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metadata = dict(
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name="GPatch",
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version="0.3.
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version="0.3.5",
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author="Adam Diehl",
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author_email="adadiehl@umich.edu",
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description="Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.",
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@@ -7,7 +7,7 @@ from Bio.Seq import Seq
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import pysam
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import random
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__version__ = "0.3.
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__version__ = "0.3.5"
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"""
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Given a name-sorted BAM file, cluster mapped reads by name and
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@@ -165,8 +165,8 @@ def main():
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parser.add_argument('-w', '--whitelist', metavar='PATH', type=str,
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required=False, default=None,
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help='Path to BED file containing whitelist regions: i.e., the inverse of blacklist regions. Supplying this will have the effect of excluding alignments that fall entirely within blacklist regions. Default=None')
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parser.add_argument('-d', '--drop_missing',
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required=False, default=False,
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parser.add_argument('-d', '--drop_missing',
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required=False, default=False, action="store_true",
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help='Omit unpatched reference chromosome records from the output if no contigs map to them. Default: Unpatched chromosomes are printed to output unchanged.')
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args = parser.parse_args()
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