refactor: pre-release cleanup (#162)

.gitignore

@@ -111,10 +111,8 @@ dmypy.json
 # Custom additions
 .vscode
 .idea
-results
 .DS_Store
 tests/.DS_Store
 results_htsinfer
 .snakemake
-tests/cluster_tests/results_sra_downloads
 *.out

README.md

@@ -32,16 +32,6 @@ example library:
 
 ```json
 {
-   "library_source": {
-      "file_1": {
-         "short_name": "hsapiens",
-         "taxon_id": "9606"
-      },
-      "file_2": {
-         "short_name": "hsapiens",
-         "taxon_id": "9606"
-      }
-   },
    "library_stats": {
       "file_1": {
          "read_length": {
@@ -62,11 +52,26 @@ example library:
          }
       }
    },
+   "library_source": {
+      "file_1": {
+         "short_name": "hsapiens",
+         "taxon_id": "9606"
+      },
+      "file_2": {
+         "short_name": "hsapiens",
+         "taxon_id": "9606"
+      }
+   },
    "library_type": {
       "file_1": "first_mate",
       "file_2": "second_mate",
       "relationship": "split_mates"
    },
+   "read_orientation": {
+      "file_1": "SF",
+      "file_2": "SR",
+      "relationship": "ISF"
+   },
    "read_layout": {
       "file_1": {
          "adapt_3": "AATGATACGGCGACC",
@@ -76,11 +81,6 @@ example library:
          "adapt_3": "AATGATACGGCGACC",
          "polyA_frac": 10.0
       }
-   },
-   "read_orientation": {
-      "file_1": "SF",
-      "file_2": "SR",
-      "relationship": "ISF"
    }
 }
 ```

htsinfer/get_library_type.py

@@ -253,18 +253,20 @@ def _update_relationship_type(self, concordant, aligned_reads):
                 self.results.relationship = (
                     StatesTypeRelationship.not_mates
                 )
-        if self.results.relationship == (
-            StatesTypeRelationship.split_mates
-        ) and (
-            self.results.file_1 == StatesType.single and
-            self.results.file_2 == StatesType.single
-        ) or (
-            self.results.file_1 == StatesType.not_available and
-            self.results.file_2 == StatesType.not_available
-        ):
-            # Update first and second relationship
-            self.results.file_1 = StatesType.first_mate_assumed
-            self.results.file_2 = StatesType.second_mate_assumed
+            if (
+                self.results.relationship == (
+                    StatesTypeRelationship.split_mates
+                )
+                and (
+                    (self.results.file_1 == StatesType.single and
+                     self.results.file_2 == StatesType.single) or
+                    (self.results.file_1 == StatesType.not_available and
+                     self.results.file_2 == StatesType.not_available)
+                )
+            ):
+                # Update first and second relationship
+                self.results.file_1 = StatesType.first_mate_assumed
+                self.results.file_2 = StatesType.second_mate_assumed
 
     class AlignedSegment:
         """Placeholder class for mypy "Missing attribute"

htsinfer/models.py

@@ -339,8 +339,8 @@ class Results(BaseModel):
         read_layout: Read layout inference results.
     """
     library_stats: ResultsStats = ResultsStats()
-    library_type: ResultsType = ResultsType()
     library_source: ResultsSource = ResultsSource()
+    library_type: ResultsType = ResultsType()
     read_orientation: ResultsOrientation = ResultsOrientation()
     read_layout: ResultsLayout = ResultsLayout()