From 5e048151d2314d8e3234cc46f73c7522d3bcb924 Mon Sep 17 00:00:00 2001
From: Mike Lin <dna@mlin.net>
Date: Wed, 15 May 2019 08:54:58 -0700
Subject: [PATCH] AttachBarcodes generic entrypoint -- fix bugs & add test
 (#66)

Fixes a few plumbing issues in the generic AttachBarcodes entry point (which allows command-line specification of the in-read positions of all barcodes). The code path with all three of (i) sample barcode in I1 fastq, (ii) cell barcode whitelist, and (iii) cell/UMI barcodes in R1 fastq as usual, had some typing issues; fixes these and tests them.
---
 src/sctools/platform.py              |  7 ++--
 src/sctools/test/test_entrypoints.py | 55 ++++++++++++++++++++++++++++
 2 files changed, 59 insertions(+), 3 deletions(-)

diff --git a/src/sctools/platform.py b/src/sctools/platform.py
index 22da63c..272b693 100644
--- a/src/sctools/platform.py
+++ b/src/sctools/platform.py
@@ -935,15 +935,16 @@ def _make_tag_generators(
         barcode_args = {'fastq_files': r1}
 
         if i1:
-            barcode_args['embedded_barcodes'] = [cls.sample_barcode]
-            tag_generators.append(fastq.EmbeddedBarcodeGenerator(**barcode_args))
+            sample_barcode_args = dict(barcode_args)
+            sample_barcode_args['embedded_barcodes'] = [cls.sample_barcode]
+            tag_generators.append(fastq.EmbeddedBarcodeGenerator(**sample_barcode_args))
 
         if whitelist:
             barcode_args['whitelist'] = whitelist
             if cls.cell_barcode:
                 barcode_args['embedded_cell_barcode'] = cls.cell_barcode
             if cls.molecule_barcode:
-                barcode_args['other_embedded_barcodes'] = cls.molecule_barcode
+                barcode_args['other_embedded_barcodes'] = [cls.molecule_barcode]
             tag_generators.append(
                 fastq.BarcodeGeneratorWithCorrectedCellBarcodes(**barcode_args)
             )
diff --git a/src/sctools/test/test_entrypoints.py b/src/sctools/test/test_entrypoints.py
index 44f114e..cb646a4 100644
--- a/src/sctools/test/test_entrypoints.py
+++ b/src/sctools/test/test_entrypoints.py
@@ -86,6 +86,61 @@ def test_Attach10XBarcodes_entrypoint_with_whitelist():
     os.remove('test_tagged_bam.bam')  # clean up
 
 
+def test_AttachBarcodes_entrypoint_with_whitelist():
+    # test of the BarcodePlatform.attach_barcodes entry point with
+    # sample, cell, and molecule barcodes all specified
+    args = [
+        '--r1',
+        data_dir + 'test_r1.fastq',
+        '--i1',
+        data_dir + 'test_i7.fastq',
+        '--u2',
+        data_dir + 'test.bam',
+        '--output-bamfile',
+        'test_tagged_bam.bam',
+        '--whitelist',
+        data_dir + '1k-august-2016.txt',
+        "--sample-barcode-start-position",
+        "0",
+        "--sample-barcode-length",
+        "8",
+        "--cell-barcode-start-position",
+        "0",
+        "--cell-barcode-length",
+        "16",
+        "--molecule-barcode-start-position",
+        "16",
+        "--molecule-barcode-length",
+        "7",  # changed 10>7 intentionally for test
+    ]
+
+    return_call = platform.BarcodePlatform.attach_barcodes(args)
+    assert return_call == 0
+    success = False
+    with pysam.AlignmentFile('test_tagged_bam.bam', 'rb', check_sq=False) as f:
+        for alignment in f:
+            if alignment.has_tag(consts.CELL_BARCODE_TAG_KEY):
+                success = True
+            # each alignment should now have a tag, and that tag should be a string
+            assert isinstance(alignment.get_tag(consts.RAW_CELL_BARCODE_TAG_KEY), str)
+            assert isinstance(
+                alignment.get_tag(consts.QUALITY_CELL_BARCODE_TAG_KEY), str
+            )
+            assert isinstance(
+                alignment.get_tag(consts.RAW_MOLECULE_BARCODE_TAG_KEY), str
+            )
+            assert len(alignment.get_tag(consts.RAW_MOLECULE_BARCODE_TAG_KEY)) == 7
+            assert isinstance(
+                alignment.get_tag(consts.QUALITY_MOLECULE_BARCODE_TAG_KEY), str
+            )
+            assert isinstance(alignment.get_tag(consts.RAW_SAMPLE_BARCODE_TAG_KEY), str)
+            assert isinstance(
+                alignment.get_tag(consts.QUALITY_SAMPLE_BARCODE_TAG_KEY), str
+            )
+    assert success
+    os.remove('test_tagged_bam.bam')  # clean up
+
+
 def test_split_bam():
     tag_args = [
         '--r1',