loqusdb 2.7.14__py3-none-any.whl → 2.7.16__py3-none-any.whl

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Files changed (7) hide show
  1. loqusdb/__init__.py +1 -1
  2. loqusdb/commands/export.py +7 -1
  3. {loqusdb-2.7.14.dist-info → loqusdb-2.7.16.dist-info}/METADATA +1 -1
  4. {loqusdb-2.7.14.dist-info → loqusdb-2.7.16.dist-info}/RECORD +7 -7
  5. {loqusdb-2.7.14.dist-info → loqusdb-2.7.16.dist-info}/LICENSE +0 -0
  6. {loqusdb-2.7.14.dist-info → loqusdb-2.7.16.dist-info}/WHEEL +0 -0
  7. {loqusdb-2.7.14.dist-info → loqusdb-2.7.16.dist-info}/entry_points.txt +0 -0
loqusdb/__init__.py CHANGED
@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
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  logger = logging.getLogger(__name__)
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- __version__ = "2.7.14"
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+ __version__ = "2.7.16"
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  INDEXES = {
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  "variant": [
loqusdb/commands/export.py CHANGED
@@ -51,7 +51,13 @@ def export(ctx, outfile, variant_type, freq):
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  for chrom in existing_chromosomes:
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  ordered_chromosomes.append(chrom)
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- nr_cases = adapter.case_count()
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+ if variant_type == "snv":
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+ nr_cases = adapter.nr_cases(snv_cases=True)
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+ elif variant_type == "sv":
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+ nr_cases = adapter.nr_cases(sv_cases=True)
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+ else:
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+ raise ValueError(f"Unknown variant_type: {variant_type}, expected 'snv' or 'sv'")
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+
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  LOG.info(f"Found {nr_cases} cases in database")
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  head = HeaderParser()
{loqusdb-2.7.14.dist-info → loqusdb-2.7.16.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: loqusdb
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- Version: 2.7.14
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+ Version: 2.7.16
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  Summary: A simple observation count database
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  License: MIT
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  Author: Your Name
{loqusdb-2.7.14.dist-info → loqusdb-2.7.16.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- loqusdb/__init__.py,sha256=_uE5d1FsrRFtBC8XjDp6UtTK1Jisma0tQStQ8gBxYWE,1688
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+ loqusdb/__init__.py,sha256=D1R2iXsppIzZJxfYNMSdRlrzsMKf-4z-tSMYAFWtEPw,1688
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  loqusdb/__main__.py,sha256=8FGKySAGaWSzAYMj6HRsxeyiME3V01Idt7HrmN7pSYY,397
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  loqusdb/build_models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  loqusdb/build_models/case.py,sha256=AByutEYK2N3kS9JFvyZfPKNZdCpZHCSD0nNHAgaU1Cs,4127
@@ -8,7 +8,7 @@ loqusdb/commands/__init__.py,sha256=BXAN3UADgqPrkGczzjlLO9GyyQ96dnLnP7n92JlYHgo,
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  loqusdb/commands/annotate.py,sha256=748kImopE5WbaO1nuv3WUgIqezWFSsi7SBeWhOz26-s,1384
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  loqusdb/commands/cli.py,sha256=wJD5S1BoCxtRTAobd1QtmQpzlngJg-mt1nsyD92fDD4,3176
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  loqusdb/commands/delete.py,sha256=R6ysHKSMw1mmL4ZbktoUIKzdzDLQ3314YPYhIy1myic,1979
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- loqusdb/commands/export.py,sha256=DPcMo4QgTCA5fu8x_IWZ9YskRl4_ikKARXpnuFr1iow,3302
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+ loqusdb/commands/export.py,sha256=HKoRzUo_BHNOdw_TcKUId9TTowi8VJVGqnuDlK-FqFE,3531
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  loqusdb/commands/identity.py,sha256=KLA9c8e6cJFDxtqIa1G6zdHTHK1sz2b3v1Utdtik_4k,787
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  loqusdb/commands/load.py,sha256=sDGCOGbukdfebLn1iBGyWoI6t3tijLzywP1tg3WheQI,4431
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  loqusdb/commands/load_profile.py,sha256=cflCbF9f77_HCH8xPnN8zSSocvIffRMnC2LPE0j7Xq8,3336
@@ -49,8 +49,8 @@ loqusdb/utils/profiling.py,sha256=3OizF7CpYvSl9kyl2g4KGJxbIRUqWfmfLxn3843XYDk,91
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  loqusdb/utils/update.py,sha256=1edJG-u24FgOSxyXAQEiyTG4IyK-Uo3lSIl5qyzcXsI,4433
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  loqusdb/utils/variant.py,sha256=U6nMZRUf5NDDQ74nG0HBCLMnFQVgFAT6eHll_F2uiwc,2087
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  loqusdb/utils/vcf.py,sha256=ybmrTBEPYa0FbUXo8ttlwATk13RnKjX9eIDbRDwCiVE,5175
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- loqusdb-2.7.14.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
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- loqusdb-2.7.14.dist-info/METADATA,sha256=BlzFtqY_6KmNyqKFLPydHC1DH059cjMi4QBb9tbwqkg,5321
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- loqusdb-2.7.14.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
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- loqusdb-2.7.14.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
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- loqusdb-2.7.14.dist-info/RECORD,,
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+ loqusdb-2.7.16.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
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+ loqusdb-2.7.16.dist-info/METADATA,sha256=Aayv73fzmF_pCfXHNoRZEzen9CbZqZccc5pfwzMXaCE,5321
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+ loqusdb-2.7.16.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
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+ loqusdb-2.7.16.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
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+ loqusdb-2.7.16.dist-info/RECORD,,