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overwrites the printableErrors option.
overwrites the printableErrors option.
--baseComposition : Print the Base Composition Statistics.
--baseComposition : Print the Base Composition Statistics.
--avgQual : Print the average phred quality per cycle & overall average quality.
--disableSeqIDCheck : Disable the unique sequence identifier check.
Use this option to save memory since the sequence id
Use this option to save memory since the sequence id
check uses a lot of memory.
check uses a lot of memory.
1 5.00 95.00 0.00 0.00 0.00 20
1 5.00 95.00 0.00 0.00 0.00 20
2 5.00 0.00 5.00 90.00 0.00 20
2 5.00 0.00 5.00 90.00 0.00 20
Phred Quality by Index are printed if --avgQual is set to ON in a version after May 29, 2012. Only valid qualities are included in these averages. For Example:
<pre>
Average Phred Quality by Read Index (starts at 0):
Read Index Average Quality
0 44.10
1 45.55
2 51.11
3 47.68
4 47.37
Overall Average Phred Quality = 50.40
</pre>
*Prints a summary of the total number of errors.
*Prints a summary of the total number of errors.
*Prints the total number of lines processed as well as the total number of sequences processed.
*Prints the total number of lines processed as well as the total number of sequences processed.
* (May 29, 2012) Average Phred Quality can be reported by cycle & overall.
