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simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
https://htseq.readthedocs.io/en/release_0.11.1/
GNU General Public License v3.0
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get_sam_line() error #52

Closed xkqqkx closed 6 years ago

xkqqkx commented 6 years ago

When calling alignment.get_sam_line() I got following error:

python3/src/HTSeq/_HTSeq.pyx in HTSeq._HTSeq.SAM_Alignment.get_sam_line()

TypeError: sequence item 9: expected str instance, bytes found

Running HTSeq v 0.9.1 with Python 3.6.4 The offending line seems to be the return call in get_sam_line() where a string is formed by joining few items (seq and qualstr field are bytes and not str).

iosonofabio commented 6 years ago

Thanks, will have a look

On April 24, 2018 1:01:31 AM PDT, xkqqkx notifications@github.com wrote:

When calling alignment.get_sam_line() I got following error:

python3/src/HTSeq/_HTSeq.pyx in
HTSeq._HTSeq.SAM_Alignment.get_sam_line()

TypeError: sequence item 9: expected str instance, bytes found

Running HTSeq v 0.9.1 with Python 3.6.4 The offending line seems to be the return call in get_sam_line() where a string is formed by joining few items (seq and qualstr field are bytes and not str).

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iosonofabio commented 6 years ago

Confirmed and fixed it in b258a15, will be there in the new release. Please use the development version until then.