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round-trip is not identical #11

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grst opened this issue Dec 20, 2018 · 4 comments
Closed

round-trip is not identical #11

grst opened this issue Dec 20, 2018 · 4 comments

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@grst
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grst commented Dec 20, 2018 •
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On some fq files, the quality string is not preserved
in a round-trip conversion. In particular ; or : gets replaced by I.

One example line, first line is original:

-BBDADFHHHHHHII?HHHIIII?EHEHCDHDHGFHHHEFHHHIECD/E?@FH1<@GEGH?GHH?@CC@?E1<D@FGH111G?CHF0CCEG?0<FFE0:F0=
+BBDADFHHHHHHII?HHHIIII?EHEHCDHDHGFHHHEFHHHIECD/E?@FH1<@GEGH?GHH?@CC@?E1<D@FGH111G?CHF0CCEG?0<FFE0IF0=

repaq-command

repaq -c -i original.fq -o original.fq.rfq
@sfchen
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sfchen commented Dec 20, 2018

Can you please upload a file, that I can test?

@grst
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grst commented Dec 20, 2018

Unfortunately, I got this file under protected access agreement.
Feel free to reach out to me by email (mail at gregor-sturm.de) and we can try to find a solution.

@sfchen
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sfchen commented Dec 20, 2018

OK

@lebovic lebovic mentioned this issue Aug 8, 2019
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@sfchen
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sfchen commented Dec 20, 2019

Should be already fixed

@sfchen sfchen closed this as completed Dec 20, 2019
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@grst @sfchen