On Wed, Oct 09, 2019 at 08:47:14AM +0000, Hannes Ponstingl wrote: > Hi Zemin, James, Andreas, > > Python was used for the test code (and internally there was a python > interface to some of the C code). > I will update that to python 3 - not a problem, just bear with me.
That's perfectly correct and it might be that just the test suite fails while smalt is perfectly fine since untouched. I tried to port these tests to Python3 with the following patch: https://salsa.debian.org/med-team/smalt/blob/master/debian/patches/2to3.patch This leads to: make check-TESTS make[4]: Entering directory '/build/smalt-0.7.6/test' PASS: splitReads_test.py PASS: results_split_test.py PASS: ouform_cigar_test.py mappings don't match for read 'SIM_000000000_MAL11_001337747_10_F_75m/1' FAIL: sample_test.py PASS: cigar_test.py Discrepancy: cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75 cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75 cigA1.mapq=60 > MAPQ_THRESH=6 and cigB1.mapq=60 > MAPQ_THRESH=6 FAIL: mthread_test.py PASS: ioform_test.py PASS: xali_test.py Traceback (most recent call last): File "./bam_cigar_test.py", line 254, in <module> isOK = testSAMfilesAreIdentical(sambamnam, samoufilnam) File "./bam_cigar_test.py", line 149, in testSAMfilesAreIdentical linA = infilA.readline() File "/usr/lib/python3.7/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 366: invalid start byte FAIL: bam_cigar_test.py ================================= 3 of 9 tests failed Please report to [email protected] ================================= Since we would really like to use the complete test suite I'd love to get this fixed. Can you help out here? Kind regards Andreas. -- http://fam-tille.de
