Merge pull request #162 from pachterlab/devel

merge devel into master

.gitignore

@@ -104,3 +104,4 @@ venv.bak/
 # mypy
 .mypy_cache/
 .DS_Store
+.vscode/

kb_python/config.py

@@ -2,7 +2,7 @@
 import platform
 import shutil
 from collections import namedtuple
-from typing import Optional
+from typing import NamedTuple, Optional
 from urllib.parse import urljoin
 
 import ngs_tools as ngs
@@ -89,12 +89,27 @@ def get_compiled_bustools_path(alias: str = COMPILED_DIR) -> Optional[str]:
 KALLISTO_PATH = get_compiled_kallisto_path() or get_provided_kallisto_path()
 BUSTOOLS_PATH = get_compiled_bustools_path() or get_provided_bustools_path()
 
+
 # Technology to file position mapping
-Technology = namedtuple('Technology', ['name', 'description', 'chemistry'])
+class Technology(NamedTuple):
+    name: str
+    description: str
+    chemistry: ngs.chemistry.Chemistry
+    show: bool = True
+
+
 TECHNOLOGIES = sorted([
     Technology('10XV1', '10x version 1', ngs.chemistry.get_chemistry('10xv1')),
     Technology('10XV2', '10x version 2', ngs.chemistry.get_chemistry('10xv2')),
     Technology('10XV3', '10x version 3', ngs.chemistry.get_chemistry('10xv3')),
+    Technology(
+        '10XV3_ULTIMA', '10x version 3 sequenced with Ultima',
+        ngs.chemistry.get_chemistry('10xv3_Ultima')
+    ),
+    Technology(
+        '10XFB', '10x Feature Barcode',
+        ngs.chemistry.get_chemistry('10xFBonly'), False
+    ),
     Technology('CELSEQ', 'CEL-Seq', ngs.chemistry.get_chemistry('celseq')),
     Technology(
         'CELSEQ2', 'CEL-SEQ version 2', ngs.chemistry.get_chemistry('celseq2')

kb_python/constants.py

@@ -16,9 +16,6 @@
 BUS_SC_FILENAME = 'output.s.c.bus'
 BUS_UNFILTERED_FILENAME = 'output.unfiltered.bus'
 BUS_FILTERED_FILENAME = 'output.filtered.bus'
-BUS_MASHED_FILENAME = 'mashed.bus'
-BUS_MERGED_FILENAME = 'merged.bus'
-ECMAP_MERGED_FILENAME = 'merged.ec'
 BUS_CDNA_PREFIX = 'spliced'
 BUS_INTRON_PREFIX = 'unspliced'
 ECMAP_FILENAME = 'matrix.ec'
@@ -63,6 +60,8 @@
 INTERNAL_SUFFIX = '_internal'
 UMI_SUFFIX = '_umi'
 CAPTURE_FILENAME = 'capture_nonUMI.txt'
+INSPECT_INTERNAL_FILENAME = 'inspect_internal.json'
+INSPECT_UMI_FILENAME = 'inspect_umi.json'
 
 # File codes.
 # These are appended to the filename whenever it undergoes some kind of