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:# Run <code>'''make clean; make'''</code> in both libStatGen and bamUtil
:# Run <code>'''make clean; make'''</code> in both libStatGen and bamUtil
:# The optimized executable is <code>'''bamUtil/bin/bam'''</code>
:# The optimized executable is <code>'''bamUtil/bin/bam'''</code>
= BamUtil: stats =
==Overflow on the pileup buffer: specifiedPosition = ####, pileup buffer start position: ####, pileup buffer end position: ####==
<pre>
Exiting due to ERROR:
Overflow on the pileup buffer: specifiedPosition = 93252, pileup buffer start position: 92227, pileup buffer end position: 93251
</pre>
:By default, bam stats assumes that a single read covers less than 1024 reference bases.
:This type of error appears if a read is longer than that. This is most likely to happen if you have large skipped regions in your CIGARs ('N's).
:You need to increase the size of the pileup buffer to cover the largest number of reference bases a single read covers.
:To fix this problem, use the <code>--bufferSize 3000</code> parameter, replacing 3000 by the appropriate number to handle the largest size of the reference covered by a read. You can increase this to a large number - it will just take up more memory.
:Future versions of bamUtil will print an additional error message including the recordName and CIGAR of the record that failed. You can use the CIGAR to come up with a better setting for <code>--bufferSize</code>, although keep in mind that future records could cover even a larger number of bases than that failing record.
:To print all of the Cigars in the file that contain an 'N' (skip), you can use (replace test.bam with your bam file):
../bin/bam findCigars --noph --cskip --in test.bam --out - |grep -v "^@" |cut -f 6
:This may help to determine a setting for <code>--bufferSize</code>.
