Opened 11 years ago

Closed 11 years ago

#240 closed Request (fixed)

Bead summary importer should have an option to fail if the number of skipped data lines get too high

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Illumina package v1.4
Component: net.sf.basedb.illumina Keywords:
Cc:

Description

The current implementation only allows a user to fail on the first "bad" line or to skip all bad lines. In some cases a small amount of "bad" lines are expected. But a larger amount may indicate a problem. See http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01795.html for some background information.

We should add an extra option (smart?) to the "Probe not found" error handler and an extra parameter that allows the user to specify a percentage or an absolute value for the maximum number of data lines to skip. If more lines with "Probe not found" are found, the plug-in should fail. The "smart" option should probably be the default selection and 5% has been suggested as the default for the threshold value.

Change History (2)

comment:1 Changed 11 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 11 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [1149]) Fixes #240: Bead summary importer should have an option to fail if the number of skipped data lines get too high

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