Fix for #42

README.md

@@ -134,6 +134,9 @@ A [preprint](https://peerj.com/preprints/2452/) is available and the submitted p
 * Consider supporting different error rates for read1 vs read2.
 * Add a ClipOverlapping modifier that will remove read overlaps (as opposed to merging).
 * Add option to InsertAdapter to trim overhangs without adapter matching.
+* Look more closely at providing solutions to the Illumina two-color chemistry issue:
+    * Provide and option to exempt G calls from the assessment of quality
+    * Trim 3′ Gs from reads
 
 ### 1.6
 

atropos/adapters/__init__.py

@@ -470,7 +470,6 @@ def random_match_probabilities(self):
         for idx, base in enumerate(seq, 1):
             cur_p *= base_probs[0 if base in c_bases else 1]
             probabilities[idx] = cur_p
-
         return probabilities
 
     def summarize(self):
@@ -484,7 +483,7 @@ def summarize(self):
             total_front=total_front,
             total_back=total_back,
             total=total_front + total_back,
-            match_probabilities=self.random_match_probabilities())
+            match_probabilities=Const(self.random_match_probabilities()))
 
         where = self.where
         assert (

atropos/align/__init__.py

@@ -205,6 +205,7 @@ def get_info_record(self):
 # 8. https://github.com/yamada-kd/nepal
 # 9. The SeqAn C++ library implements several alignment algorithms: 
 # http://www.sciencedirect.com/science/article/pii/S0168165617315420
+# 10. Could we treat paired end read + adapter alignment as an MSA problem?
 
 class InsertAligner(object):
     """Implementation of an insert matching algorithm.

atropos/commands/detect/__init__.py

@@ -34,6 +34,7 @@
 # ntCard https://github.com/bcgsc/ntCard
 # https://github.com/TGAC/KAT
 # https://arxiv.org/pdf/1707.01743.pdf
+# https://github.com/splatlab/squeakr
 
 # TODO: In KnownContaminantDetector, accept template sequences with wildcards
 # to match against.

tests/test_align.py

@@ -152,7 +152,7 @@ def test_insert_align():
     assert match1.length == 10
     assert match2.rstart == 20
     assert match2.length == 10
-    
+
 def test_short_adapter_overlap():
     a1_seq = 'TTAGACATAT'
     a2_seq = 'CAGTGGAGTA'
@@ -165,6 +165,19 @@ def test_short_adapter_overlap():
     assert match2.rstart == 28
     assert match2.length == 2
 
+def test_insert_align_different_lengths():
+    # Test for #51. This is the alignment:
+    # TTAGGCTATGGCTTCTCGGGTTGAGGCTACAAGTTTTGGACCCTCCAGAGCAAAGCAGGTCTCTTTGACATCAGCTGCACAGCACTTGTCTACAAAAGCTGCAAA
+    #                                                                                                                       AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
+    # ATAGGCTATGGCTTCTCGAGTTGAAGCTACAAGTTTTGGACCCTCCAGAGCAAAGCAGGTCTCTTTGACATCAGCTGCACAGCACTTGTCTACAAAAGCTGCAAAAGATCGGAAGAGCGTCTCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGACGTATCATTAAAAAAAAAAACACATCACATCAACAAGATAACACGACTTCTCCATCCACAGTACCGATGACCTCAACATTAGT
+    #
+    # The inserts should align even though there is a gap at the 5' end of read1.
+    a1_seq = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG'
+    a2_seq = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
+    seq1 = 'TTTGCAGCTTTTGTAGACAAGTGCTGTGCAGCTGATGTCAAAGAGACCTGCTTTGCTCTGGAGGGTCCAAAACTTGTAGCCTCAACCCGAGAAGCCATAGCCTAA'
+    seq2 = 'ATAGGCTATGGCTTCTCGAGTTGAAGCTACAAGTTTTGGACCCTCCAGAGCAAAGCAGGTCTCTTTGACATCAGCTGCACAGCACTTGTCTACAAAAGCTGCAAAAGATCGGAAGAGCGTCTCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGACGTATCATTAAAAAAAAAAACACATCACATCAACAAGATAACACGACTTCTCCATCCACAGTACCGATGACCTCAACATTAGT'
+
+
 def test_multi_aligner_no_mismatches():
     from atropos.align._align import MultiAligner
     a = MultiAligner(max_error_rate=0, min_overlap=3)