termination in gemini annotate. closes
MODIFY
docs/content/history.rst
docs/content/history.rst
@@ -11,6 +11,7 @@ Release History
#. Initial support for python 3.
#. Support annotating with bcftools BCSQ (http://biorxiv.org/content/early/2016/12/01/090811) in addition to VEP and SnpEff.
#. Fix bug that resulted in the message: `UnsupportedOperation: IOStream has no fileno.` when loading. (Thanks Andrew O. and Ryan R.)
+#. Fix bug where gemini annotate would never finish (see: arq5x/gemini#809 (Thanks @mmoisse)
0.19.1
======

MODIFY
gemini/gemini_annotate.py
gemini/gemini_annotate.py
@@ -97,6 +97,7 @@ def _annotate_variants(args, conn, metadata, get_val_fn, col_names=None, col_typ
select_res = cursor.execution_options(stream_results=True).execute('''SELECT chrom, start, end, ref, alt, variant_id FROM variants''')
while True:
+
for row in select_res.fetchmany(CHUNK_SIZE):
# update_data starts out as a list of the values that should
@@ -126,6 +127,7 @@ def _annotate_variants(args, conn, metadata, get_val_fn, col_names=None, col_typ
print("updated", total, "variants")
last_id = current_id
to_update = []
+ print("finished updating", total, "variants")
def _update_variants(metadata, to_update, col_names, cursor):
tbl = metadata.tables["variants"]

termination in gemini annotate. closes #809.