better error reporting on parse errors about cutadapt HOT 8 CLOSED

From [email protected] on March 18, 2011 00:57:32

Could you please send me (or attach to this issue) the first few lines of the TEE.TEST.fastq file?

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From [email protected] on March 18, 2011 11:15:13

Cutadapt runs and removes the adapter sequence but does not report statistics.

Attachment: TEE.TEST.fastq

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From [email protected] on March 18, 2011 11:26:06

The issue must have been with that file, when I ran it with the full data set it worked fine. Sorry to have bothered you. Thank you for your help.

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From [email protected] on March 18, 2011 14:27:56

No need to be sorry, cutadapt could at least give a better error message. It seems that your test file contains two unexpected empty lines in the end, and this must have caused the assertion error. I will leave this issue open until I have added better error reporting to the routines that read in FASTQ files.

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From [email protected] on March 18, 2011 14:28:51

Summary: better error reporting on parse errors

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From [email protected] on April 20, 2011 09:50:08

This issue was closed by revision r133 .

Status: Fixed

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From [email protected] on April 20, 2011 09:52:04

I've added some slightly better error reporting. Now cutadapt reports this when confronted with your file:
Error: at line 253, expected a line starting with '+'

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From [email protected] on April 20, 2011 09:55:53

Thanks! Much appreciated.

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