Fix documentation inaccuracies across codebase (#146)

- LocusRead.reference_positions: base-1 → base-0 (#128)
- run_isovar docstring: fix param name decompress_threads → decompression_threads,
  fix return type "Generator" → "list of IsovarResult" (#129)
- README: protein_sequence_matches_predicted_effect →
  protein_sequence_matches_predicted_mutation_effect (#133)
- DataFrameBuilder.exclude docstring: "should be used" → "should be omitted" (#135)

Fixes #128, #129, #133, #135

Author: iskandr

README.md

@@ -170,7 +170,7 @@ A variant which fails one or more filters is not excluded from the result collec
 If a result collection is flattened into a DataFrame then each filter is included as a column. 
 
 It's also possible to filter on boolean properties (without numerical thresholds) by passing `filter_flags` to `run_isovar`. These boolean
-properties can be further negated by prepending 'not_' to the property name, so that both `'protein_sequence_matches_predicted_effect'` and `'not_protein_sequence_matches_predicted_effect'` are valid names for `filter_flags`.
+properties can be further negated by prepending 'not_' to the property name, so that both `'protein_sequence_matches_predicted_mutation_effect'` and `'not_protein_sequence_matches_predicted_mutation_effect'` are valid names for `filter_flags`.
 
 ## Commandline 
 

isovar/__init__.py

@@ -10,7 +10,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-__version__ = "1.4.9"
+__version__ = "1.4.10"
 
 
 from .allele_read import AlleleRead

isovar/dataframe_builder.py

@@ -49,8 +49,8 @@ def __init__(
             named '_fields' which is a list of field names.
 
         exclude : set
-            Field names from element_class which should be used as columns for
-            the DataFrame we're building
+            Field names from element_class which should be omitted from the
+            DataFrame we're building
 
         converters : dict
             Dictionary of names mapping to functions. These functions will be

isovar/locus_read.py

@@ -55,7 +55,7 @@ def __init__(
             cDNA sequence
 
         reference_positions : list of (int or None)
-            For every base in the sequence, which base-1 reference position
+            For every base in the sequence, which base-0 reference position
             does it map to, or None if the read base is an insertion or soft-clipped
 
         quality_scores : array of int

isovar/main.py

@@ -122,13 +122,15 @@ def run_isovar(
         they can also be negated by prepending "not_",
         such as "not_has_protein_sequence".
 
-    decompress_threads : int
+    decompression_threads : int
         Number of threads used by htslib to decompress BAM/CRAM
         files.
 
-    Generator of IsovarResult objects, one for each variant. The
-    `protein_sequences` field of the IsovarVar result will be empty
-    if no sequences could be determined.
+    Returns
+    -------
+    list of IsovarResult
+        One per variant. The `protein_sequences` field will be empty
+        if no sequences could be determined.
     """
     if filter_thresholds is None:
         filter_thresholds = OrderedDict(DEFAULT_FILTER_THRESHOLDS)