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A colleague and I noticed that FastQC 0.11.2
(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trimmomatic
0.32 (http://www.usadellab.org/cms/?page=trimmomatic) had problems with many
.bz2 files that were compressed with pbzip2. I traced this to an issue with the
bundled jbzip2 0.9.0, though I verified that the issue is present in both
jbzip2 0.9.1 and the current trunk (revision r43) as well.
The attached file (Clean_Miseq_S3_R1.fastq.bz2) was compressed with pbzip2
1.1.8, using the -p1 option to avoid the chance of encountering any latent
race-condition bug triggered by the use of multiple threads:
$ pbzip2 -p1 Clean_Miseq_S3_R1.fastq
bzip2 1.0.6 has no problem has no problem decompressing this file:
$ bzcat < Clean_Miseq_S3_R1.fastq.bz2 > Clean_Miseq_S3_R1.test-bzip2.fastq
$ ls -l Clean_Miseq_S3_R1.test-bzip2.fastq
-rw-rw-r-- 1 foo foo 36497333 Dec 12 13:15 Clean_Miseq_S3_R1.test-bzip2.fastq
However, the jbzip2 0.9.1 demo.Decompress exits with status 0, but results in a
truncated file whose size appears to correspond to the default bzip2 900k block
size:
$ java -cp jbzip2-0.9.1.jar demo.Decompress Clean_Miseq_S3_R1.fastq.bz2
$ echo $?
0
$ ls -l Clean_Miseq_S3_R1.fastq
-rw-rw-r-- 1 foo foo 900000 Dec 12 13:16 Clean_Miseq_S3_R1.fastq
jbzip2 0.9.1 has no problem decompressing the file when compressed with bzip2:
$ bzip2 Clean_Miseq_S3_R1.test-bzip2.fastq
$ java -cp jbzip2-0.9.1.jar demo.Decompress
Clean_Miseq_S3_R1.test-bzip2.fastq.bz2
$ ls -l Clean_Miseq_S3_R1.test-bzip2.fastq
-rw-rw-r-- 1 foo foo 36497333 Dec 12 13:18 Clean_Miseq_S3_R1.test-bzip2.fastq
--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
Crop Genome Informatics Laboratory
Iowa State University
http://weeks.public.iastate.edu/
https://www.linkedin.com/in/nweeks
Original issue reported on code.google.com by [email protected]
on 12 Dec 2014 at 7:21
Attachments:
Please see the attached patch. This will help with publishing artifacts to
Maven Central via SontaType OSSRH.
It essentially introduces a pom.xml file and implements the typical expects
Maven directory structure e.g. src/main/java.
From top directory in trunk, it can be applied as follows
patch -p0 -i bzip2.maven.patch
You can then build the project by invoking
$ cd jbzip2/
$ mvn install
Original issue reported on code.google.com by [email protected]
on 21 Apr 2015 at 11:18
Attachments:
What steps will reproduce the problem?
We run a very complex mapped object tree, with several levels of nested objects
in lists, where each list can contain large amounts (thousands) of objects.
Dozer handles this without a problem, but of course - very slowly.
Orika's overhead is negligable to non-existant (we map objects that are about
2-4 mb of binary data usually under 1 ms). so performance wise it's very good.
anyhow - it seems that from time to time an object from a different path in the
object tree get's mapped to the wrong list:
i.e.
myObject.myList<FirstType>.nestedList<NestedType>
would get objects from
myObject.otherList<SecondType>
the really strange thing is that nested list would contain mostly NestedType an
one instance of SecondType
reproduction is consistent when a large enough object tree (say 2-3 levels of
nesting, thousands of objects in the lists) and enough executions of the mapper.
out of 800 mappings of the root object i consistently get 3-4 class cast
exceptions while iterating on those lists.
This seems to happen only after the code has been compiled into byte code -
that's my diagnosis based on the fact that it happens very intermittently, and
far more frequently on "run" configuration rather than on "debug".
i would say that it was a race-condition but i am running on a single thread so
i don't see how that would be possible. but that might be all-together
unrelated.
What version of the product are you using? On what operating system?
we're using the latest 1.2.0 version, but this goes back as at lest 1.1.5 which
was the first version we tried. i check every release to see if it was resolved.
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 8 Sep 2012 at 10:26
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