Merge branch 'dev' into 'master'

Merge dev into master for release 0.5.3

See merge request tron/easyquant!25

.gitlab-ci.yml

@@ -1,6 +1,14 @@
 stages:
+  - build
   - test
-  - deploy
+
+build_pipeline:
+  image: condaforge/mambaforge:23.3.1-0
+  stage: build
+  script:
+    - mamba env create -f environment.yml --prefix conda_env/
+    - source /opt/conda/bin/activate conda_env/
+    - pip install .
 
 test_pipeline:
   image: condaforge/mambaforge:23.3.1-0
@@ -9,11 +17,6 @@ test_pipeline:
     - mamba env create -f environment.yml --prefix conda_env/
     - source /opt/conda/bin/activate conda_env/
     - pip install .
+    - python -m unittest tests/tests.py
     - bash run_test.sh
 
-deploy-job:      # This job runs in the deploy stage.
-  stage: deploy  # It only runs when *both* jobs in the test stage complete successfully.
-  environment: production
-  script:
-    - echo "Deploying application..."
-    - echo "Application successfully deployed."

README.md

@@ -188,6 +188,7 @@ Using the interval mode the output will look slightly different:
 | HPRT1         | 400_793  | 0                          | 0                       | 974             | 0.98          | 126.40        | 101.0           |
 
 
+Hint: This is just an example to illustrate the design of the table. Results may differ.
 
 
 #### Columns in output file

example_data/CLDN18_Context_seq.csv

@@ -5,3 +5,5 @@ CLDN18_total;CATGCTGCAGGCAGTGCGAGCCCTGATGATCGTAGGCATCGTCCTGGGTGCCATTGGCCTCCTGGTA
 CLDN18_1_fake;CCTTGAACCAGGAGCGAAACTGAGCTATCTAAGGAAAACACTGTGAGCAAATACTGAGAGCCTAGGGAAACCATCTGATTAGAAGAGCTCCCCTCAGGAGCGCGTTAGCTTCACACCTTCGGCAGCAGGAGGGCGGCAGCTTCTCGCAGGCGGCAGGGCGGGCGGCCAGGATCATGTCCACCACCACATGCCAAGTGGTGGCGTTCCTCCTGTCCATCCTGGGGCTGGCCGGCTGCATCGCGGCCACCGGGATGGACATGTGGAGCACCCAGGACCTGTACGACAACCCCGTCACCTCCGTGTTCCAGTACGAAGGGCTCTGGAGGAGCTGCGTGAGGCAGAGTTCAGGCTTCACCGAATGCAGGCCCTATTTCACCATCCTGGGACTTCCAGCTACAAAGCCGTTTCTTATCATGCCTCAGGCCACAGTGTTGCCTACAAGCCTGGAGGCTTCAAGGCCAGCACTGGCTTTGGGTCCAACACCAAAAACAAGAAGATATACGATGGAGGTGCCCGCACAGAGGACGAGGTACAATCTTATCCTTCCAAGCACGACTATGTGTAATGCTCTAAGACCTCTCAGCACGGGCGGAAGAAACTCCCGGAGAGCTCACCCAAAAAACAAGGAGATCCCATCTAGATTTCTTCTTGCTTTTGACTCACAGCTGGAAGTTAGAAAAGCCTCGATTTCATCTTTGGAGAGGCCAAATGGTCTTAGCCTCAGTCTCTGTCTCTAAATATTCCACCATAAAACAGCTGAGTTATTTATGAATTAGAGGCTATAGC;400
 CLDN18_2_fake;AACCGCCTCCATTACATGGTCCGTTCCTGACGTGTACACCAGCCTCTCAGAGAAAACTCCATCCCTACACTCGGTAGTCTCAGAATTGCGCTGTCCACTTGTCGTGTGGCTCTGTGTCGACACTGTGCGCCACCATGGCCGTGACTGCCTGTCAGGGCTTGGGGTTCGTGGTTTCACTGATTGGGATTGCGGGCATCATTGCTGCCACCTGCATGGACCAGTGGAGCACCCAAGACTTGTACAACAACCCCGTAACAGCTGTTTTCAACTACCAGGGGCTGTGGCGCTCCTGTGTCCGAGAGAGCTCTGGCTTCACCGAGTGCCGGGGCTACTTCACCCTGCTGGGGCTGCCAGCTACAAAGCCGTTTCTTATCATGCCTCAGGCCACAGTGTTGCCTACAAGCCTGGAGGCTTCAAGGCCAGCACTGGCTTTGGGTCCAACACCAAAAACAAGAAGATATACGATGGAGGTGCCCGCACAGAGGACGAGGTACAATCTTATCCTTCCAAGCACGACTATGTGTAATGCTCTAAGACCTCTCAGCACGGGCGGAAGAAACTCCCGGAGAGCTCACCCAAAAAACAAGGAGATCCCATCTAGATTTCTTCTTGCTTTTGACTCACAGCTGGAAGTTAGAAAAGCCTCGATTTCATCTTTGGAGAGGCCAAATGGTCTTAGCCTCAGTCTCTGTCTCTAAATATTCCACCATAAAACAGCTGAGTTATTTATGAATTAGAGGCTATAGC;361
 HPRT1;GGGCTATAAATTCTTTGCTGACCTGCTGGATTACATCAAAGCACTGAATAGAAATAGTGATAGATCCATTCCTATGACTGTAGATTTTATCAGACTGAAGAGCTATTGTAATGACCAGTCAACAGGGGACATAAAAGTAATTGGTGGAGATGATCTCTCAACTTTAACTGGAAAGAATGTCTTGATTGTGGAAGATATAATTGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACCCCACGAAGTGTTGGATATAAGCCAGACTTTGTTGGATTTGAAATTCCAGACAAGTTTGTTGTAGGATATGCCCTTGACTATAATGAATACTTCAGGGATTTGAATCATGTTTGTGTCATTAGTGAAACTGGAAAAGCAAAATACAAAGCCTAAGATGAGAGTTCAAGTTGAGTTTGGAAACATCTGGAGTCCTATTGACATCGCCAGTAAAATTATCAATGTTCTAGTTCTGTGGCCATCTGCTTAGTAGAGCTTTTTGCATGTATCTTCTAAGAATTTTATCTGTTTTGTACTTTAGAAATGTCAGTTGCTGCATTCCTAAACTGTTTATTTGCACTATGAGCCTATAGACTATCAGTTCCCTTTGGGCGGATTGTTGTTTAACTTGTAAATGAAAAAATTCTCTTAAACCACAGCACTATTGAGTGAAACATTGAACTCATATCTGTAAGAAATAAAGAGAAGATATATTAGTTTTTTAATTGGTATTTTAATTTT;400
+HPRT1_dup;GGGCTATAAATTCTTTGCTGACCTGCTGGATTACATCAAAGCACTGAATAGAAATAGTGATAGATCCATTCCTATGACTGTAGATTTTATCAGACTGAAGAGCTATTGTAATGACCAGTCAACAGGGGACATAAAAGTAATTGGTGGAGATGATCTCTCAACTTTAACTGGAAAGAATGTCTTGATTGTGGAAGATATAATTGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACCCCACGAAGTGTTGGATATAAGCCAGACTTTGTTGGATTTGAAATTCCAGACAAGTTTGTTGTAGGATATGCCCTTGACTATAATGAATACTTCAGGGATTTGAATCATGTTTGTGTCATTAGTGAAACTGGAAAAGCAAAATACAAAGCCTAAGATGAGAGTTCAAGTTGAGTTTGGAAACATCTGGAGTCCTATTGACATCGCCAGTAAAATTATCAATGTTCTAGTTCTGTGGCCATCTGCTTAGTAGAGCTTTTTGCATGTATCTTCTAAGAATTTTATCTGTTTTGTACTTTAGAAATGTCAGTTGCTGCATTCCTAAACTGTTTATTTGCACTATGAGCCTATAGACTATCAGTTCCCTTTGGGCGGATTGTTGTTTAACTTGTAAATGAAAAAATTCTCTTAAACCACAGCACTATTGAGTGAAACATTGAACTCATATCTGTAAGAAATAAAGAGAAGATATATTAGTTTTTTAATTGGTATTTTAATTTT;400
+HPRT1_similar;GGGCTATAAATTCTTTGCTGACCTGCTGGATTACATCAAAGCACTGAATAGACATAGTGATAGATCCATTCCTATGACTGTAGATTTTATCAGACTGAAGAGCTATTGTAATGACCAGTCAACAGGGGACATAAAAGTAATTGGTGGAGATGATCTCTCAACTTTAACTGGAAAGAATGTCTTGATTGTGGAAGATATAATTGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACCCCACGAAGTGTTGGATATAAGCCAGACTTTGTTGGATTTGAAATTCCAGACAAGTTTGTTGTAGGATATGCCCTTGACTATAATGAATACTTCAGGGATTTGAATCATGTTTGTGTCATTAGTGAAACTGGAAAAGCAAAATACAGAGCCTAAGATGAGAGTTCAAGTTGAGTTTGGAAACATCTGGAGTCCTATTGACATCGCCAGTAAAATTATCAATGTTCTAGTTCTGTGGCCACCTGCTTAGTAGAGCTTTTTGCATGTATCTTCTAAGAATTTTATCTGTTTTGTACTTTAGAAATGTCAGTTGCTGCATTCCTAAACTGTTTATTTGCACTATGAGCCTATAGACTATCAGTTCCCTAAGGGCGGATTGTTGTTTAACTTGTAAATGAAAAAATTCTCTTAAACCACAGCACTATTGAGTGAAACATTGAACTCATATCTGTAAGAAATAAAGAGAAGATATATTAGTTTTTTAATTGGTATTTTAATTTT;400

example_data/CLDN18_Context_seq.tsv

@@ -5,3 +5,5 @@ CLDN18_total	CATGCTGCAGGCAGTGCGAGCCCTGATGATCGTAGGCATCGTCCTGGGTGCCATTGGCCTCCTGGTA
 CLDN18_1_fake	CCTTGAACCAGGAGCGAAACTGAGCTATCTAAGGAAAACACTGTGAGCAAATACTGAGAGCCTAGGGAAACCATCTGATTAGAAGAGCTCCCCTCAGGAGCGCGTTAGCTTCACACCTTCGGCAGCAGGAGGGCGGCAGCTTCTCGCAGGCGGCAGGGCGGGCGGCCAGGATCATGTCCACCACCACATGCCAAGTGGTGGCGTTCCTCCTGTCCATCCTGGGGCTGGCCGGCTGCATCGCGGCCACCGGGATGGACATGTGGAGCACCCAGGACCTGTACGACAACCCCGTCACCTCCGTGTTCCAGTACGAAGGGCTCTGGAGGAGCTGCGTGAGGCAGAGTTCAGGCTTCACCGAATGCAGGCCCTATTTCACCATCCTGGGACTTCCAGCTACAAAGCCGTTTCTTATCATGCCTCAGGCCACAGTGTTGCCTACAAGCCTGGAGGCTTCAAGGCCAGCACTGGCTTTGGGTCCAACACCAAAAACAAGAAGATATACGATGGAGGTGCCCGCACAGAGGACGAGGTACAATCTTATCCTTCCAAGCACGACTATGTGTAATGCTCTAAGACCTCTCAGCACGGGCGGAAGAAACTCCCGGAGAGCTCACCCAAAAAACAAGGAGATCCCATCTAGATTTCTTCTTGCTTTTGACTCACAGCTGGAAGTTAGAAAAGCCTCGATTTCATCTTTGGAGAGGCCAAATGGTCTTAGCCTCAGTCTCTGTCTCTAAATATTCCACCATAAAACAGCTGAGTTATTTATGAATTAGAGGCTATAGC	400
 CLDN18_2_fake	AACCGCCTCCATTACATGGTCCGTTCCTGACGTGTACACCAGCCTCTCAGAGAAAACTCCATCCCTACACTCGGTAGTCTCAGAATTGCGCTGTCCACTTGTCGTGTGGCTCTGTGTCGACACTGTGCGCCACCATGGCCGTGACTGCCTGTCAGGGCTTGGGGTTCGTGGTTTCACTGATTGGGATTGCGGGCATCATTGCTGCCACCTGCATGGACCAGTGGAGCACCCAAGACTTGTACAACAACCCCGTAACAGCTGTTTTCAACTACCAGGGGCTGTGGCGCTCCTGTGTCCGAGAGAGCTCTGGCTTCACCGAGTGCCGGGGCTACTTCACCCTGCTGGGGCTGCCAGCTACAAAGCCGTTTCTTATCATGCCTCAGGCCACAGTGTTGCCTACAAGCCTGGAGGCTTCAAGGCCAGCACTGGCTTTGGGTCCAACACCAAAAACAAGAAGATATACGATGGAGGTGCCCGCACAGAGGACGAGGTACAATCTTATCCTTCCAAGCACGACTATGTGTAATGCTCTAAGACCTCTCAGCACGGGCGGAAGAAACTCCCGGAGAGCTCACCCAAAAAACAAGGAGATCCCATCTAGATTTCTTCTTGCTTTTGACTCACAGCTGGAAGTTAGAAAAGCCTCGATTTCATCTTTGGAGAGGCCAAATGGTCTTAGCCTCAGTCTCTGTCTCTAAATATTCCACCATAAAACAGCTGAGTTATTTATGAATTAGAGGCTATAGC	361
 HPRT1	GGGCTATAAATTCTTTGCTGACCTGCTGGATTACATCAAAGCACTGAATAGAAATAGTGATAGATCCATTCCTATGACTGTAGATTTTATCAGACTGAAGAGCTATTGTAATGACCAGTCAACAGGGGACATAAAAGTAATTGGTGGAGATGATCTCTCAACTTTAACTGGAAAGAATGTCTTGATTGTGGAAGATATAATTGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACCCCACGAAGTGTTGGATATAAGCCAGACTTTGTTGGATTTGAAATTCCAGACAAGTTTGTTGTAGGATATGCCCTTGACTATAATGAATACTTCAGGGATTTGAATCATGTTTGTGTCATTAGTGAAACTGGAAAAGCAAAATACAAAGCCTAAGATGAGAGTTCAAGTTGAGTTTGGAAACATCTGGAGTCCTATTGACATCGCCAGTAAAATTATCAATGTTCTAGTTCTGTGGCCATCTGCTTAGTAGAGCTTTTTGCATGTATCTTCTAAGAATTTTATCTGTTTTGTACTTTAGAAATGTCAGTTGCTGCATTCCTAAACTGTTTATTTGCACTATGAGCCTATAGACTATCAGTTCCCTTTGGGCGGATTGTTGTTTAACTTGTAAATGAAAAAATTCTCTTAAACCACAGCACTATTGAGTGAAACATTGAACTCATATCTGTAAGAAATAAAGAGAAGATATATTAGTTTTTTAATTGGTATTTTAATTTT	400
+HPRT1_dup	GGGCTATAAATTCTTTGCTGACCTGCTGGATTACATCAAAGCACTGAATAGAAATAGTGATAGATCCATTCCTATGACTGTAGATTTTATCAGACTGAAGAGCTATTGTAATGACCAGTCAACAGGGGACATAAAAGTAATTGGTGGAGATGATCTCTCAACTTTAACTGGAAAGAATGTCTTGATTGTGGAAGATATAATTGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACCCCACGAAGTGTTGGATATAAGCCAGACTTTGTTGGATTTGAAATTCCAGACAAGTTTGTTGTAGGATATGCCCTTGACTATAATGAATACTTCAGGGATTTGAATCATGTTTGTGTCATTAGTGAAACTGGAAAAGCAAAATACAAAGCCTAAGATGAGAGTTCAAGTTGAGTTTGGAAACATCTGGAGTCCTATTGACATCGCCAGTAAAATTATCAATGTTCTAGTTCTGTGGCCATCTGCTTAGTAGAGCTTTTTGCATGTATCTTCTAAGAATTTTATCTGTTTTGTACTTTAGAAATGTCAGTTGCTGCATTCCTAAACTGTTTATTTGCACTATGAGCCTATAGACTATCAGTTCCCTTTGGGCGGATTGTTGTTTAACTTGTAAATGAAAAAATTCTCTTAAACCACAGCACTATTGAGTGAAACATTGAACTCATATCTGTAAGAAATAAAGAGAAGATATATTAGTTTTTTAATTGGTATTTTAATTTT	400
+HPRT1_similar	GGGCTATAAATTCTTTGCTGACCTGCTGGATTACATCAAAGCACTGAATAGACATAGTGATAGATCCATTCCTATGACTGTAGATTTTATCAGACTGAAGAGCTATTGTAATGACCAGTCAACAGGGGACATAAAAGTAATTGGTGGAGATGATCTCTCAACTTTAACTGGAAAGAATGTCTTGATTGTGGAAGATATAATTGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACCCCACGAAGTGTTGGATATAAGCCAGACTTTGTTGGATTTGAAATTCCAGACAAGTTTGTTGTAGGATATGCCCTTGACTATAATGAATACTTCAGGGATTTGAATCATGTTTGTGTCATTAGTGAAACTGGAAAAGCAAAATACAGAGCCTAAGATGAGAGTTCAAGTTGAGTTTGGAAACATCTGGAGTCCTATTGACATCGCCAGTAAAATTATCAATGTTCTAGTTCTGTGGCCACCTGCTTAGTAGAGCTTTTTGCATGTATCTTCTAAGAATTTTATCTGTTTTGTACTTTAGAAATGTCAGTTGCTGCATTCCTAAACTGTTTATTTGCACTATGAGCCTATAGACTATCAGTTCCCTAAGGGCGGATTGTTGTTTAACTTGTAAATGAAAAAATTCTCTTAAACCACAGCACTATTGAGTGAAACATTGAACTCATATCTGTAAGAAATAAAGAGAAGATATATTAGTTTTTTAATTGGTATTTTAATTTT	400

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "bp_quant"
-version = "0.5.2"
+version = "0.5.3"
 authors = [
   {name = "TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz", email = "[email protected]"},
 ]
@@ -43,4 +43,4 @@ dependencies = {file = ["requirements.txt"]}
 Homepage = "https://github.com/tron-bioinformatics/easyquant"
 
 [project.scripts]
-bp_quant = "bp_quant.command_line:bp_quant_cli"
+bp_quant = "bp_quant.command_line:bp_quant_cli"

src/bp_quant/aligning.py

@@ -1,15 +1,22 @@
 import subprocess
 
-
-def get_align_cmd_bowtie2(fq1, fq2, index_dir, out_dir, num_threads):
-    cmd = "bowtie2 -p {0} -x {1}/bowtie -1 {2} -2 {3} -S {4}/Aligned.out.sam".format(
-        num_threads,
-        index_dir,
-        fq1,
-        fq2,
-        out_dir
-    )
-
+def get_align_cmd_bowtie2(fq1, fq2, bam, index_dir, out_dir, num_threads):
+    cmd=""
+    if fq1 and fq2:
+        cmd = "bowtie2 -p {0} -x {1}/bowtie -a --end-to-end -1 {2} -2 {3} -S {4}/Aligned.out.sam".format(
+            num_threads,
+            index_dir,
+            fq1,
+            fq2,
+            out_dir
+        )
+    elif not fq1 and not fq2 and bam:
+        cmd = "bowtie2 -p {0} -x {1}/bowtie -a --end-to-end -b {2} --align-paired-reads -S {3}/Aligned.out.sam".format(
+            num_threads,
+            index_dir,
+            bam,
+            out_dir
+        ) 
     return cmd
 
 
@@ -79,7 +86,7 @@ def get_align_cmd_star(fq1, fq2, bam, index_dir, out_dir, num_threads, custom_pa
 def run(fq1, fq2, bam, index_dir, out_path, threads, method, params):
     cmd = None
     if method == "bowtie2":
-        cmd = get_align_cmd_bowtie2(fq1, fq2, index_dir, out_path, threads)
+        cmd = get_align_cmd_bowtie2(fq1, fq2, bam, index_dir, out_path, threads)
     elif method == "bwa":
         cmd = get_align_cmd_bwa(fq1, fq2, index_dir, out_path, threads)
     elif method == "star":

src/bp_quant/pipeline.py

@@ -18,7 +18,7 @@ def __get_read_count_fq(fq_file):
     """Parses input FASTQ to get read count"""
     ps = subprocess.Popen(("zcat", fq_file), stdout=subprocess.PIPE)
     result = subprocess.check_output(("wc", "-l"), stdin=ps.stdout)
-    return int(result) / 2
+    return int(result) / 4
 
 
 def __get_read_count_bam(bam_file):
@@ -111,10 +111,11 @@ def run(self, method, num_threads, align_cmd_params):
         quant_file = os.path.join(self.working_dir, "quantification.tsv")
         num_reads_file = os.path.join(self.working_dir, "num_reads.txt")
         # Define files to be deleted after successful run
-        clean_up_files = [genome_path, fasta_file, sam_file]
+        clean_up_files = [genome_path, sam_file]
         if not self.keep_aln:
             clean_up_files.append(cram_file)
             clean_up_files.append("{}.crai".format(cram_file))
+            clean_up_files.append(fasta_file)
 
         #create folders
         IOMethods.create_folder(align_path)

src/bp_quant/requantify.py

@@ -189,7 +189,7 @@ def parse_alignment(self):
 
         for read in bam.fetch():
 
-            if read.flag > 255:
+            if read.flag > 511:
                 continue
             # Handle missing reference sequences which occur in SAM/BAM
             # but not in seq_table.csv

src/bp_quant/version.py

@@ -1,2 +1,2 @@
-version_info = (0, 5, 2)
+version_info = (0, 5, 3)
 version = '.'.join(str(c) for c in version_info)

tests/tests.py

@@ -5,7 +5,7 @@
 
 SEQ_TABLE_FILE = os.path.join("example_data", "CLDN18_Context_seq.csv")
 
-from easy_quant.requantify import perc_true, get_seq_to_pos, classify_read
+from bp_quant.requantify import perc_true, get_seq_to_pos, classify_read
 
 
 class TestRequantify(unittest.TestCase):
@@ -40,6 +40,14 @@ def test_get_seq_to_pos(self):
             'HPRT1':[
                 ('0_400', 0, 400),
                 ('400_793', 400, 793)
+            ],
+            'HPRT1_dup':[
+                ('0_400', 0, 400),
+                ('400_793', 400, 793)
+            ],
+            'HPRT1_similar':[
+                ('0_400', 0, 400),
+                ('400_793', 400, 793)
             ]
         }
         self.assertEqual(get_seq_to_pos(SEQ_TABLE_FILE), result)
@@ -51,7 +59,7 @@ def test_classify_read(self):
             ('0_400', 0, 400),
             ('400_786', 400, 786)
         ]
-        result = {"junc": True, "within": False, "interval": "0_400", "anchor": 15}
+        result = {"junc": True, "within": False, "interval": "0_400", "anchor": 15, "nm_in_bp_area": 0}
         self.assertEqual(classify_read(365, 415, aln_pairs, interval, True, 10), result)
 
 
@@ -61,7 +69,7 @@ def test_classify_read(self):
             ('0_400', 0, 400),
             ('400_786', 400, 786)
         ]
-        result = {"junc": False, "within": True, "interval": "400_786", "anchor": 0}
+        result = {"junc": False, "within": True, "interval": "400_786", "anchor": 0, "nm_in_bp_area": 0}
         self.assertEqual(classify_read(609, 658, aln_pairs, interval, True, 10), result)
 
 
@@ -133,7 +141,7 @@ def test_classify_read(self):
             ('0_200', 0, 200),
             ('200_400', 200, 400)
         ]
-        result = {"junc": True, "interval": "0_200", "within": False, "anchor": 22}
+        result = {"junc": True, "interval": "0_200", "within": False, "anchor": 22, "nm_in_bp_area": 0}
         self.assertEqual(classify_read(172, 222, aln_pairs, interval, True, 10), result)