Error on duplicates in augur parse

Previously, augur parse would let duplicates pass silently with the following behavior:

- sequence output contains all duplicates
- metadata output contains only the last occurrence of duplicates

The behavior is unintentional and undocumented.

This small change will immediately raise an error and exit when a duplicate is detected.

augur/parse.py

@@ -5,7 +5,7 @@
 import sys
 
 from .io import open_file, read_sequences, write_sequences
-from .utils import get_numerical_date_from_value
+from .utils import AugurError, get_numerical_date_from_value
 
 forbidden_characters = str.maketrans(
     {' ': None,
@@ -176,6 +176,8 @@ def run(args):
                 args.prettify_fields,
                 args.fix_dates
             )
+            if sequence_record.id in meta_data:
+                raise AugurError(f"Duplicate found for '{sequence_record.id}'.")
             meta_data[sequence_record.id] = sequence_metadata
 
             sequences_written = write_sequences(

tests/functional/parse.t

@@ -31,4 +31,22 @@ Parse compressed Zika sequences into sequences and metadata.
   $ diff -u "parse/metadata.tsv" "$TMP/metadata.tsv"
   $ rm -f "$TMP/sequences.fasta" "$TMP/metadata.tsv"
 
+Error on the first duplicate.
+
+  $ echo -e '> SEQ1' >> $TMP/data.fasta
+  $ echo -e 'AAA'    >> $TMP/data.fasta
+  $ echo -e '> SEQ1' >> $TMP/data.fasta
+  $ echo -e 'AAA'    >> $TMP/data.fasta
+  $ echo -e '> SEQ2' >> $TMP/data.fasta
+  $ echo -e 'AAA'    >> $TMP/data.fasta
+  $ echo -e '> SEQ2' >> $TMP/data.fasta
+  $ echo -e 'AAA'    >> $TMP/data.fasta
+  $ ${AUGUR} parse \
+  >   --sequences $TMP/data.fasta \
+  >   --output-sequences "$TMP/sequences.fasta" \
+  >   --output-metadata "$TMP/metadata.tsv" \
+  >   --fields strain
+  ERROR: Duplicate found for 'SEQ1'.
+  [2]
+
   $ popd > /dev/null