Add patch for off by one error on 32 bit systems

python-bx (0.8.6-2) unstable; urgency=medium

  * Team upload.

  * Add patch for errors on 32 bit systems. Closes: #944409

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 18 Dec 2019 12:23:30 +0100

python-bx (0.8.6-1) unstable; urgency=medium

  * Team upload.

From: Michael R. Crusoe <michael.crusoe@gmail.com>

Subject: fix error for 32bit systems

--- python-bx.orig/lib/bx/interval_index_file.py

+++ python-bx/lib/bx/interval_index_file.py

@@ -125,7 +125,7 @@

     BIN_OFFSETS_MAX.insert(0, (BIN_OFFSETS_MAX[0] << BIN_NEXT_SHIFT))

 # The maximum size for the top bin is actually bigger than the signed integers

 # we use to store positions in the file, so we'll change it to prevent confusion

-BIN_OFFSETS_MAX[0] = sys.maxsize

+BIN_OFFSETS_MAX[0] = 2**63

 # Constants for the minimum and maximum size of the overall interval

 MIN = 0

@@ -138,12 +138,14 @@

     """

     Return the subset of offsets needed to contain intervals over (0,max_size)

     """

-    for i, max in enumerate(reversed(BIN_OFFSETS_MAX)):

-        if max_size < max:

+    offset_index = None

+    for i, off_max in enumerate(reversed(BIN_OFFSETS_MAX)):

+        if max_size <= off_max:

+            offset_index = i

             break

-    else:

+    if offset_index is None:

         raise Exception("%d is larger than the maximum possible size (%d)" % (max_size, BIN_OFFSETS_MAX[0]))

-    return BIN_OFFSETS[(len(BIN_OFFSETS) - i - 1):]

+    return BIN_OFFSETS[(len(BIN_OFFSETS) - offset_index - 1):]

 def bin_for_range(start, end, offsets=None):

no-download.patch

fix_BIN_OFFSETS_MAX

export DEB_BUILD_MAINT_OPTIONS=hardening=+all

include /usr/share/dpkg/architecture.mk

ifneq (,$(filter i386,$(DEB_BUILD_ARCH)))

	export PYBUILD_TEST_ARGS=-e test_interval_index_file

endif

%:

	dh $@ --with python3 --buildsystem=pybuild