Fix reverse position calculation in Sequence.py

NEWS.rst

@@ -1,6 +1,14 @@
 Release Notes
 ================================================================================
 
+Version 0.7.9dev
+-------------------------------------------------------------------------------
+
+MaskPrimers:
+
++ Fixed a bug in MaskPrimers align involving the reverse primer position offset 
+calculation.
+
 Version 0.7.8: January 28, 2026
 -------------------------------------------------------------------------------
 

presto/Sequence.py

@@ -903,7 +903,7 @@ def localAlignment(seq_record, primers, primers_regex=None, max_error=default_as
             align.end = align_coord[0][-1]
         else:
             # Count position from tail and end gaps
-            rev_pos = rec_len - align_coord[0][-1]
+            rev_pos = rec_len - max_len if rec_len > max_len else 0
             align.start = rev_pos + align_coord[0][0]
             align.end = rev_pos + align_coord[0][-1]
 

presto/Version.py

@@ -5,5 +5,5 @@
 __author__    = 'Jason Anthony Vander Heiden'
 __copyright__ = 'Copyright 2026 Kleinstein Lab, Yale University. All rights reserved.'
 __license__   = 'GNU Affero General Public License 3 (AGPL-3)'
-__version__   = '0.7.8'
+__version__   = '0.7.9dev'
 __date__      = '2026.01.28'

tests/test_MaskPrimers.py

@@ -200,6 +200,45 @@ def test_localAlignment(self):
         self.assertListEqual([(x, round(y, 4)) for x, y in self.align_indel],
                              [(x.primer, round(x.error, 4)) for x in align])
 
+    def test_issue110_revprimer_cut(self):
+        """Test reverse primer alignment with maxlen parameter (issue #110)"""
+        # Test case from issue #110: reverse primer alignment
+        # This is equivalent to:
+        # MaskPrimers.py align --mode cut --revpr --skiprc --maxerror 0.2 --maxlen 800
+
+        # Input sequence
+        seq = Seq('ATGTCAGTTAGCTCGTTCAGGTAATAGTTGCCCACACAACGTCAAAATAAGAGAACGGTCGTAACATTATCCGTGATTTTCTCACTACTATCAGTACTCACGACTCGACTCTGCCGCAGCCACGTATCGCCTGAAAGCCAGTCAGCGTTAAGGAGTGCTCTGAGCAGGACAACTCGCGTAGTGAGAGTTACATGTTCGTTGGGCTCTTCCGACACGGACCTGAGTTGGCCAACGTCCCACCTGAGGTCTGTGCCCCGGTGATGAGAAGTGTGCATCTCGTTCTTGCAGCTCGTCAGTACTTTCAGAATCATGGCGTGCATGGTAGAATGACCCTTATAACGGACTTCGACATGGCAATAACCCCCCGTTTCTACTTCTAGAGGAGAAAAGTATTGACATGAGCGCTCCCGGCACAAGGGCCAAAGAAGTCTCCAATTTCTTATTTCCGAATGACATGCGTCTCCTTGCGGGTAAATCACCGACCGCAATTCATAGAAGCCTGGGGGAACAGATAGGTCTAATTAGCTTAAGAGAGTAAATCCTGGGATCATCGATACTAGTTGTTTTATATTTGTTGTAAAAAGTAGTAATTACTTCAGTAGTAACCATAAACTTACGCTGGGGCTTCTTCGGCGGATTTTTACAGTTACCAACCAGGAGATTTGAAGTAAATCAGTTGAGGATTTAGCCGCGCTATCCGGTAATCTCCAAATTAAAACATACCGTTCCATGAAGGCTAGAATTAC')
+        record = SeqRecord(seq, id='sample4')
+
+        # PGK1 reverse complement primer - looking for it at the end of the sequence
+        primers = OrderedDict([('PGK1', 'CGATACTAGTTGTTTTATATTTGTTGTAAAAAGTAGATAATTACT')])
+
+        # Test with maxlen parameter, rev_primer=True, skip_rc=True
+        score_dict = getDNAScoreDict(mask_score=(0, 1), gap_score=(0, 0))
+        result = localAlignment(record, primers, max_error=0.2, max_len=800, 
+                               rev_primer=True, skip_rc=True, score_dict=score_dict)
+
+        print('\nTEST issue #110 reverse primer>')
+        print('       ID> %s' % result.seq.id)
+        print('   PRIMER> %s' % result.primer)
+        print(' REV_PRIM> %s' % result.rev_primer)
+        print('  PRSTART> %d' % result.start)
+        print('    ERROR> %.4f' % result.error)
+
+        # Verify the alignment found the reverse primer
+        # Position should be 551 (1-based, as shown in the log output)
+        self.assertEqual(result.primer, 'PGK1')
+        self.assertTrue(result.rev_primer)
+        self.assertEqual(result.start, 551)
+        self.assertAlmostEqual(result.error, 0.0444, places=3)
+        self.assertTrue(result.valid)
+
+        # Test the cut operation - verify the sequence is trimmed correctly
+        cut_seq = maskSeq(result, mode='cut', barcode=False)
+        expected_cut = 'ATGTCAGTTAGCTCGTTCAGGTAATAGTTGCCCACACAACGTCAAAATAAGAGAACGGTCGTAACATTATCCGTGATTTTCTCACTACTATCAGTACTCACGACTCGACTCTGCCGCAGCCACGTATCGCCTGAAAGCCAGTCAGCGTTAAGGAGTGCTCTGAGCAGGACAACTCGCGTAGTGAGAGTTACATGTTCGTTGGGCTCTTCCGACACGGACCTGAGTTGGCCAACGTCCCACCTGAGGTCTGTGCCCCGGTGATGAGAAGTGTGCATCTCGTTCTTGCAGCTCGTCAGTACTTTCAGAATCATGGCGTGCATGGTAGAATGACCCTTATAACGGACTTCGACATGGCAATAACCCCCCGTTTCTACTTCTAGAGGAGAAAAGTATTGACATGAGCGCTCCCGGCACAAGGGCCAAAGAAGTCTCCAATTTCTTATTTCCGAATGACATGCGTCTCCTTGCGGGTAAATCACCGACCGCAATTCATAGAAGCCTGGGGGAACAGATAGGTCTAATTAGCTTAAGAGAGTAAATCCTGGGATCAT'
+        print('  CUT_SEQ> %s' % cut_seq.seq)
+        self.assertEqual(str(cut_seq.seq), expected_cut)
+
     #@unittest.skip('-> maskSeq() skipped\n')
     def test_maskSeq(self):
         print('TEST CUT>')