libsnappy1.0.3 and picard-tools ok
Hi,
I have just uploaded libsnappy1.0.3-java_1.0.3-rc3~dfsg-3 which does
not conflict anymore on maven repo.
I use it against picard-tools, with additiona patches for jbzip2 usage
and classpath issue and it seems to work.
Charles,
follows test output. I do not know if it is ok (at least no error).
Git repo is up-to-date if you want to build the package.
If ok, do you upload the package or do you want I do it?
# picard-tools EstimateLibraryComplexity
I=testdata/net/sf/samtools/compressed.bam O=/dev/stdout
[Mon Sep 03 08:49:13 CEST 2012]
net.sf.picard.sam.EstimateLibraryComplexity
INPUT=[testdata/net/sf/samtools/compressed.bam] OUTPUT=/dev/stdout
MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20
MAX_GROUP_RATIO=500
READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*
OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false
VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Sep 03 08:49:13 CEST 2012] Executing as root@debiansid on Linux
3.0.0-1-amd64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard
version: 1.75(exported)
INFO 2012-09-03 08:49:13 EstimateLibraryComplexity Will store
826115 read pairs in memory before sorting.
INFO 2012-09-03 08:49:14 EstimateLibraryComplexity Finished
reading - moving on to scanning for duplicates.
## net.sf.picard.metrics.StringHeader
# net.sf.picard.sam.EstimateLibraryComplexity
INPUT=[testdata/net/sf/samtools/compressed.bam] OUTPUT=/dev/stdout
MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20
MAX_GROUP_RATIO=500
READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*
OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false
VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## net.sf.picard.metrics.StringHeader
# Started on: Mon Sep 03 08:49:13 CEST 2012
[Mon Sep 03 08:49:14 CEST 2012]
net.sf.picard.sam.EstimateLibraryComplexity done. Elapsed time: 0.01
minutes.
Runtime.totalMemory()=15925248
Olivier
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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