Merge 3662159 into f9d5fc7

hammerlab · Jul 12, 2017 · 07bcca2 · 07bcca2
2 parents f9d5fc7 + 3662159
commit 07bcca2
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 182 deletions.
diff --git a/cohorts/cohort.py b/cohorts/cohort.py
@@ -643,7 +643,12 @@ def _load_single_patient_merged_variants(self, patient, use_cache=True):
             for patient_variants in patient.variants_list:
                 if type(patient_variants) == str:
                     if ".vcf" in patient_variants:
-                        variant_collections.append(varcode.load_vcf_fast(patient_variants))
+                        try:
+                            variant_collections.append(varcode.load_vcf_fast(patient_variants))
+                        except StopIteration as e:
+                            logger.warning('Error loading VCFs for patient '+
+                                             '{} {}'.format(patient.id,
+                                                             str(e)))
                     elif ".maf" in patient_variants:
                         # See variant_stats.maf_somatic_variant_stats
                         variant_collections.append(

diff --git a/cohorts/io/__init__.py b/cohorts/io/__init__.py
diff --git a/cohorts/io/gcloud_storage.py b/cohorts/io/gcloud_storage.py
diff --git a/requirements.txt b/requirements.txt
@@ -18,4 +18,3 @@ serializable>=0.0.8
 dill>=0.2.5
 tqdm>=4.10.0
 pysam>=0.9.0
-google-cloud-storage>=1.1.1