fixes

marine.py

@@ -380,7 +380,7 @@ def generate_depths_with_samtools(output_folder, bam_filepaths):
     for i, bam_filepath in enumerate(bam_filepaths):
         depth_command = (
         "echo 'running samtools depth on {}...';"
-        "samtools depth -b {}/combined.bed {} >> {}/coverage/depths.txt"
+        "samtools depth -a -g 0x704 -b {}/combined.bed {} >> {}/coverage/depths.txt"
     ).format(bam_filepath, output_folder, bam_filepath, output_folder)
         all_depth_commands.append(depth_command)
 
@@ -888,7 +888,7 @@ def check_samtools():
                   "\tFor single-cell: \t{} contigs at at time\n".format(num_per_sublist)
                  ])
 
-    if not barcode_tag and not paired_end:
+    if not paired_end:
         # Check to see that samtools is available in the environment
         check_samtools()
 

src/read_process.py

@@ -189,7 +189,8 @@ def get_read_information(read, contig, barcode_tag='CB', verbose=False, stranded
     if read.is_duplicate:
         return 'is_duplicate', [], {}
 
-
+    if read.is_supplementary:
+        return 'is_supplementary', [], {}
     #if 'N' in cigarstring:
     #    return 'N', [], {}
 

tests/integration_tests.ipynb

@@ -2889,7 +2889,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "id": "f5c3ed3e-13dd-4399-924e-3d1ac17ce387",
    "metadata": {},
    "outputs": [