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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
