BamUtil: FAQ - Revision history

Mktrost at 17:04, 23 September 2014

2014-09-23T17:04:46Z

← Older revision		Revision as of 13:04, 23 September 2014
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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>.

Mktrost at 13:49, 25 March 2014

2014-03-25T13:49:34Z

@@ Line 1: / Line 1: @@
 __TOC__
 = Compile Problems =
@@ Line 17: / Line 19: @@
 # Set CXX11_AVAIL = 0 in your environment
 By making one of these changes, the code should compile and use map instead of unordered_map.

Mktrost: /* HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’ */

2013-05-01T14:42:08Z

HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’

← Older revision		Revision as of 10:42, 1 May 2013
Line 10:		Line 10:
	</pre>		</pre>
	: HashErrorModel by default uses an unordered_map which is only found in C++11/C++0x.		: HashErrorModel by default uses an unordered_map which is only found in C++11/C++0x.
	: The code attempts to automatically detect whether or not you have C++11/C++0x by checking if the ~~CCVERSION~~ > X4.3.0.		: The code attempts to automatically detect whether or not you have C++11/C++0x by checking if the gcc version > X4.3.0.
	: If you see this failure, that means this check did not properly work and you will need to manually disable the C++11/C++0x code. There are a couple of ways to do this:		: If you see this failure, that means this check did not properly work and you will need to manually disable the C++11/C++0x code. There are a couple of ways to do this:
	# Update bamUtil/Makefile.inc, line 7, change <code>CXX11_AVAIL ?= 1</code> to <code>CXX11_AVAIL = 0</code>		# Update bamUtil/Makefile.inc, line 7, change <code>CXX11_AVAIL ?= 1</code> to <code>CXX11_AVAIL = 0</code>

Mktrost: /* HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’ */

2013-05-01T13:35:08Z

HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’

← Older revision		Revision as of 09:35, 1 May 2013
Line 11:		Line 11:
	: HashErrorModel by default uses an unordered_map which is only found in C++11/C++0x.		: HashErrorModel by default uses an unordered_map which is only found in C++11/C++0x.
	: The code attempts to automatically detect whether or not you have C++11/C++0x by checking if the CCVERSION > X4.3.0.		: The code attempts to automatically detect whether or not you have C++11/C++0x by checking if the CCVERSION > X4.3.0.
	: If you see this failure, that means this check did not properly work ~~for~~ you~~. You~~ will need to manually disable the C++11/C++0x code. There are a couple of ways to do this:		: If you see this failure, that means this check did not properly work and you will need to manually disable the C++11/C++0x code. There are a couple of ways to do this:
	# Update bamUtil/Makefile.inc, line 7, change <code>CXX11_AVAIL ?= 1</code> to <code>CXX11_AVAIL = 0</code>		# Update bamUtil/Makefile.inc, line 7, change <code>CXX11_AVAIL ?= 1</code> to <code>CXX11_AVAIL = 0</code>
	# Set CXX11_AVAIL to 0 on the command line:		# Set CXX11_AVAIL to 0 on the command line:

Mktrost: Created page with '__TOC__ = Compile Problems = ==HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’== : Error:

 Hash…'

2013-05-01T13:31:56Z

Created page with '__TOC__ = Compile Problems = ==HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’== : Error: <pre> Hash…'

New page

__TOC__

= Compile Problems =
==HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’==
: Error:
<pre>
HashErrorModel.cpp: In member function ‘uint8_t HashErrorModel::getQemp(BaseData&)’:
HashErrorModel.cpp:96: error: ‘class std::unordered_map, std::equal_to, std::allocator > >’ has no member named ‘at’
make[2]: *** [../obj/HashErrorModel.o] Error 1
</pre>
: HashErrorModel by default uses an unordered_map which is only found in C++11/C++0x.
: The code attempts to automatically detect whether or not you have C++11/C++0x by checking if the CCVERSION > X4.3.0.
: If you see this failure, that means this check did not properly work for you. You will need to manually disable the C++11/C++0x code. There are a couple of ways to do this:
# Update bamUtil/Makefile.inc, line 7, change <code>CXX11_AVAIL ?= 1</code> to <code>CXX11_AVAIL = 0</code>
# Set CXX11_AVAIL to 0 on the command line:
#: <pre>make CXX11_AVAIL=0</pre>
# Set CXX11_AVAIL = 0 in your environment
By making one of these changes, the code should compile and use map instead of unordered_map.