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Description: test_BWA_tool.py: update to bwa 0.7.19 header.
This change fixes/worksaround the following test failure, which has
begun to appear with the introduction of bwa 0.7.19:
.
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Tests/test_BWA_tool.py", line 203, in test_mem
self.assertTrue(
~~~~~~~~~~~~~~~^
headline.startswith("@SQ"),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
AssertionError: False is not true : Error generating sam files:
bwa mem BWA/human_g1k_v37_truncated.fasta BWA/HNSCC1_1_truncated.fastq BWA/HNSCC1_2_truncated.fastq
Output starts:@HD VN:1.5 SO:unsorted GO:query
.
This test failure occurs in a portion that has been obsoleted upstream,
therefore no forwarding was possible in that regard.
Author: Étienne Mollier <emollier@debian.org>
Bug: https://github.com/biopython/biopython/pull/5063
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114298
Last-Update: 2025-09-13
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-biopython.orig/Tests/test_BWA_tool.py
+++ python-biopython/Tests/test_BWA_tool.py
@@ -161,7 +161,7 @@
with open(self.samfile1) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ") or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
)
@@ -184,7 +184,7 @@
with open(self.samfile) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ") or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
)
@@ -201,7 +201,7 @@
with open(self.samfile) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ") or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
)
|
