{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/523","repository_url":"https://api.github.com/repos/samtools/htsjdk","labels_url":"https://api.github.com/repos/samtools/htsjdk/issues/523/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/523/comments","events_url":"https://api.github.com/repos/samtools/htsjdk/issues/523/events","html_url":"https://github.com/samtools/htsjdk/issues/523","id":141619577,"number":523,"title":"Errors inflating Intel deflated bams.","user":{"login":"jacarey","id":6933549,"avatar_url":"https://avatars.githubusercontent.com/u/6933549?v=3","gravatar_id":"","url":"https://api.github.com/users/jacarey","html_url":"https://github.com/jacarey","followers_url":"https://api.github.com/users/jacarey/followers","following_url":"https://api.github.com/users/jacarey/following{/other_user}","gists_url":"https://api.github.com/users/jacarey/gists{/gist_id}","starred_url":"https://api.github.com/users/jacarey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jacarey/subscriptions","organizations_url":"https://api.github.com/users/jacarey/orgs","repos_url":"https://api.github.com/users/jacarey/repos","events_url":"https://api.github.com/users/jacarey/events{/privacy}","received_events_url":"https://api.github.com/users/jacarey/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/samtools/htsjdk/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":null,"comments":17,"created_at":"2016-03-17T15:37:29Z","updated_at":"2016-03-17T22:57:39Z","closed_at":null,"body":"Bams generated after https://github.com/samtools/htsjdk/pull/515 are causing issues when we try to inflate them.\r\n\r\n@mishalinaik  @akiezun \r\n\r\n[Thu Mar 17 11:22:51 EDT 2016] picard.sam.ValidateSamFile INPUT=test3.bam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json\r\n[Thu Mar 17 11:22:51 EDT 2016] Executing as jcarey@jcarey-OptiPlex-7010 on Linux 4.2.0-34-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_66-internal-b17; Picard version: 1eccaab927be982f02d61cc3bc5ad2b9617a4e9f JdkDeflater\r\n[Thu Mar 17 11:22:52 EDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.02 minutes.\r\nRuntime.totalMemory()=253231104\r\nTo get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp\r\n\r\nException in thread \"main\" htsjdk.samtools.util.RuntimeIOException: java.util.zip.DataFormatException: invalid block type\r\n\tat htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112)\r\n\tat htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:410)\r\n\tat htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:392)\r\n\tat htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)\r\n\tat htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:260)\r\n\tat htsjdk.samtools.SamStreams.readBytes(SamStreams.java:24)\r\n\tat htsjdk.samtools.SamStreams.isBAMFile(SamStreams.java:58)\r\n\tat htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:255)\r\n\tat htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:134)\r\n\tat picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:154)\r\n\tat picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)\r\n\tat picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)\r\n\tat edu.mit.broad.picard.cmdline.PicardPrivateCommandLine.main(PicardPrivateCommandLine.java:24)\r\nCaused by: java.util.zip.DataFormatException: invalid block type\r\n\tat java.util.zip.Inflater.inflateBytes(Native Method)\r\n\tat java.util.zip.Inflater.inflate(Inflater.java:259)\r\n\tat htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)\r\n\t... 12 more"},"comment":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/comments/198116502","html_url":"https://github.com/samtools/htsjdk/issues/523#issuecomment-198116502","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/523","id":198116502,"user":{"login":"jacarey","id":6933549,"avatar_url":"https://avatars.githubusercontent.com/u/6933549?v=3","gravatar_id":"","url":"https://api.github.com/users/jacarey","html_url":"https://github.com/jacarey","followers_url":"https://api.github.com/users/jacarey/followers","following_url":"https://api.github.com/users/jacarey/following{/other_user}","gists_url":"https://api.github.com/users/jacarey/gists{/gist_id}","starred_url":"https://api.github.com/users/jacarey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jacarey/subscriptions","organizations_url":"https://api.github.com/users/jacarey/orgs","repos_url":"https://api.github.com/users/jacarey/repos","events_url":"https://api.github.com/users/jacarey/events{/privacy}","received_events_url":"https://api.github.com/users/jacarey/received_events","type":"User","site_admin":false},"created_at":"2016-03-17T22:57:39Z","updated_at":"2016-03-17T22:57:39Z","body":"@lbergelson Not using the Intel Deflater no."}}