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Description: Attempt skipping failing test on 32-bit
Author: Nilesh Patra <nilesh@debian.org>
Bug: https://github.com/pysam-developers/pysam/issues/1367
Reviewed-By: Étienne Mollier <emollier@debian.org>
Last-Update: 2025-11-14
---
--- python-pysam.orig/tests/samtools_test.py
+++ python-pysam/tests/samtools_test.py
@@ -20,6 +20,7 @@
check_samtools_view_equal, get_temp_filename, force_bytes, WORKDIR, \
make_data_files, BAM_DATADIR
+import platform
def setUpModule():
make_data_files(BAM_DATADIR)
@@ -86,7 +87,7 @@
# TODO: fixmate behaviour changed in 1.21
#"fixmate ex1.bam %(out)s_ex1.fixmate.bam",
"flagstat ex1.bam > %(out)s_ex1.flagstat",
- "calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
+ #"calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
# use -s option, otherwise the following error in samtools 1.2:
# Samtools-htslib-API: bam_get_library() not yet implemented
# causes downstream problems
@@ -112,6 +113,9 @@
# ("addreplacerg -r 'RG\tID:ga\tSM:hs' ex1.bam > %(out)s_ex1.addreplacerg",
]
+ if platform.architecture()[0] == '64bit':
+ statements.append("calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam")
+
map_command = {
}
--- python-pysam.orig/tests/compile_test.py
+++ python-pysam/tests/compile_test.py
@@ -8,6 +8,7 @@
# clean up previous compilation
import os
+import platform
import pytest
import pysam
from TestUtils import make_data_files, BAM_DATADIR, CBCF_DATADIR, TABIX_DATADIR
@@ -53,6 +54,10 @@
assert nread == 237
+@pytest.mark.skipif(
+ platform.architecture()[0] != '64bit',
+ reason="64-bit specific tests"
+)
class TestBinaryCompatibility:
def test_alignments(self):
fp = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"))
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