Merge branch 'develop' into enhance-file-parsing

# Conflicts:
#	tests/__init__.py

.travis.yml

@@ -9,35 +9,26 @@ language: python
 
 before_install:
   - pip install --upgrade pip setuptools wheel
-  - pip install pytest-cov codecov awscli
+  - pip install pytest-cov codecov
 
 install:
   - pip install .
 
 script:
-  # for testing, limit downloads from the resource servers by using cached resources;
-  # note that the master branch is tested weekly via `cron`, so this ensures all Python
-  # versions will be periodically integration tested with the resource servers
+  # for testing, limit downloads from the resource servers to only the selected job for
+  # PRs and the master branch; note that the master branch is tested weekly via `cron`,
+  # so this ensures all Python versions will be periodically integration tested with the
+  # resource servers
   - set -e
   - NUM_JOBS=4
   - SELECTED_JOB=$((10#$(date +%V) % $NUM_JOBS))  # identify a job based on week of the year
-  - DOWNLOADS_ENABLED=false
   - |
-    if [[ $TRAVIS_PULL_REQUEST != "false" ]]; then
-      # download resources for all jobs on a pull request
-      DOWNLOADS_ENABLED=true
+    if [[ $TRAVIS_PULL_REQUEST != "false" && $SELECTED_JOB == $JOB_ID ]]; then
+      # download resources for selected job on a pull request
+      export DOWNLOADS_ENABLED=true
     elif [[ $TRAVIS_BRANCH == "master" && $SELECTED_JOB == $JOB_ID ]]; then
       # download resources for selected job on master branch
-      DOWNLOADS_ENABLED=true
-    fi
-  - |
-    if [[ $DOWNLOADS_ENABLED == "false" ]]; then
-      # use cached resources on Amazon S3
-      aws s3 cp s3://snps-resources/resources.tar.gz resources.tar.gz
-      if [[ -f resources.tar.gz ]]; then
-        tar -xzf resources.tar.gz
-        rm resources.tar.gz
-      fi
+      export DOWNLOADS_ENABLED=true
     fi
   - pytest --cov=snps tests
   - |

src/snps/resources.py

@@ -520,33 +520,8 @@ def _get_path_assembly_mapping_data(
         if not create_dir(self._resources_dir):
             return ""
 
-        chroms = [
-            "1",
-            "2",
-            "3",
-            "4",
-            "5",
-            "6",
-            "7",
-            "8",
-            "9",
-            "10",
-            "11",
-            "12",
-            "13",
-            "14",
-            "15",
-            "16",
-            "17",
-            "18",
-            "19",
-            "20",
-            "21",
-            "22",
-            "X",
-            "Y",
-            "MT",
-        ]
+        chroms = [str(i) for i in range(1, 23)]
+        chroms.extend(["X", "Y", "MT"])
 
         assembly_mapping_data = source_assembly + "_" + target_assembly
         destination = os.path.join(

src/snps/snps.py

@@ -143,6 +143,7 @@ def __init__(
 
                 if assign_par_snps:
                     self._assign_par_snps()
+                    self.sort_snps()
             else:
                 logger.warning("no SNPs loaded...")
 
@@ -897,6 +898,9 @@ def remap_snps(self, target_assembly, complement_bases=True):
         ----------
         1. Ensembl, Assembly Map Endpoint,
            http://rest.ensembl.org/documentation/info/assembly_map
+        2. Yates et. al. (doi:10.1093/bioinformatics/btu613),
+           `<http://europepmc.org/search/?query=DOI:10.1093/bioinformatics/btu613>`_
+        3. Zerbino et. al. (doi.org/10.1093/nar/gkx1098), https://doi.org/10.1093/nar/gkx1098
         """
         chromosomes_remapped = []
         chromosomes_not_remapped = []
@@ -997,8 +1001,8 @@ def _remapper(self, task):
         for mapping in mappings["mappings"]:
             # skip if mapping is outside of range of SNP positions
             if (
-                mapping["original"]["end"] <= pos_start
-                or mapping["original"]["start"] >= pos_end
+                mapping["original"]["end"] < pos_start
+                or mapping["original"]["start"] > pos_end
             ):
                 continue