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Hi,
the mzML writer uses a second pass when writing indexed mzML. This silently produces incorrect output if the target is not a proper file:
FileConverter -in LCMS-centroided.mzML -write_scan_index true -out_type mzML -out /dev/stdout | tail
<offset idRef="spectrum=108">2</offset>
<offset idRef="spectrum=109">2</offset>
<offset idRef="spectrum=110">2</offset>
<offset idRef="spectrum=111">2</offset>
<offset idRef="spectrum=112">2</offset>
</index>
</indexList>
<indexListOffset>-1</indexListOffset>
<fileChecksum>0</fileChecksum>
</indexedmzML>FileConverter took 0.16 s (wall), 0.16 s (CPU), 0.02 s (system), 0.14 s (user); Peak Memory Usage: 43 MB.
sneumann@msbi-corei:/tmp$ echo $?
0
The for indexed mzML, writer could check that the target is a real file and 1) give an appropriate error message 2) a non-zero exit code otherwise.
Yours, Steffen
The text was updated successfully, but these errors were encountered:
Hi,
the mzML writer uses a second pass when writing indexed mzML. This silently produces incorrect output if the target is not a proper file:
The for indexed mzML, writer could check that the target is a real file and 1) give an appropriate error message 2) a non-zero exit code otherwise.
Yours, Steffen
The text was updated successfully, but these errors were encountered: