Merge pull request #201 from joachimwolff/scool

[WIP] Scool format support
open2c · Jul 14, 2020 · 16afcb8 · 16afcb8
2 parents d14db63 + 0dc7d8c
commit 16afcb8
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Showing 12 changed files with 559 additions and 29 deletions.
diff --git a/cooler/__init__.py b/cooler/__init__.py
@@ -12,7 +12,7 @@
 """
 from ._version import __version__, __format_version__
 from .api import Cooler, annotate
-from .create import create_cooler, rename_chroms
+from .create import create_cooler, rename_chroms, create_scool
 from .reduce import merge_coolers, coarsen_cooler, zoomify_cooler
 from .balance import balance_cooler
 from .util import binnify, read_chromsizes, fetch_chromsizes

diff --git a/cooler/_version.py b/cooler/_version.py
@@ -1,2 +1,4 @@
-__version__ = "0.8.8"
+__version__ = "0.8.8-dev"
 __format_version__ = 3
+__format_version_scool__ = 1
+
diff --git a/cooler/create/__init__.py b/cooler/create/__init__.py
@@ -2,6 +2,8 @@
 import numpy as np
 
 MAGIC = u"HDF5::Cooler"
+MAGIC_SCOOL = u"HDF5::SCOOL"
+
 URL = u"https://github.com/mirnylab/cooler"
 CHROM_DTYPE = np.dtype("S")
 CHROMID_DTYPE = np.int32
@@ -28,4 +30,4 @@
     ContactBinner,
 )
 
-from ._create import create_cooler, create, create_from_unordered, append, rename_chroms
+from ._create import create_cooler, create, create_from_unordered, append, rename_chroms, create_scool