{"action":"closed","number":622,"pull_request":{"url":"https://api.github.com/repos/genome/genome/pulls/622","id":32549426,"html_url":"https://github.com/genome/genome/pull/622","diff_url":"https://github.com/genome/genome/pull/622.diff","patch_url":"https://github.com/genome/genome/pull/622.patch","issue_url":"https://api.github.com/repos/genome/genome/issues/622","number":622,"state":"closed","locked":false,"title":"Update GMT::Picard::CheckIlluminaDirectory","user":{"login":"iferguson90","id":633311,"avatar_url":"https://avatars.githubusercontent.com/u/633311?v=3","gravatar_id":"","url":"https://api.github.com/users/iferguson90","html_url":"https://github.com/iferguson90","followers_url":"https://api.github.com/users/iferguson90/followers","following_url":"https://api.github.com/users/iferguson90/following{/other_user}","gists_url":"https://api.github.com/users/iferguson90/gists{/gist_id}","starred_url":"https://api.github.com/users/iferguson90/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iferguson90/subscriptions","organizations_url":"https://api.github.com/users/iferguson90/orgs","repos_url":"https://api.github.com/users/iferguson90/repos","events_url":"https://api.github.com/users/iferguson90/events{/privacy}","received_events_url":"https://api.github.com/users/iferguson90/received_events","type":"User","site_admin":false},"body":"It now uses `GMT::Picard::Base`.\r\n\r\nWe don't seem to use this module anywhere in Genome. Talking to @thepler it doesn't seem like LIMS is actively using it either.\r\n\r\nWe could remove the module altogether, although it's so simple now it doesn't seem particularly harmful to keep it around. It also currently has no tests. Unfortunately there doesn't seem to be much we can test beyond just running the tool. Todd pointed me to some ~~test~~ **production** data that works... it's several gigabytes:\r\n\r\n```\r\n$ gmt picard check-illumina-directory --basecalls-directory \"$HOME/links/check-illumina-dir-example/Data/Intensities/BaseCalls\" --use-version 1.113 --lane 1 --read-structure 151T6B\r\nUsing libraries at /gscuser/iferguso/git/genome/master/lib/perl\r\nRUN: java -Xmx4096m -XX:MaxPermSize=64m -cp /usr/share/java/ant.jar:/usr/share/java/picard-tools1.113/CheckIlluminaDirectory.jar net.sf.picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/gscuser/iferguso/links/check-illumina-dir-example/Data/Intensities/BaseCalls LANES=1 MAX_RECORDS_IN_RAM=500000 READ_STRUCTURE=151T6B TMP_DIR=/tmp/gm-genome_sys-2015-04-02_15_54_06--uKe5/Picard-FXPp VALIDATION_STRINGENCY=SILENT\r\n[Thu Apr 02 15:54:06 CDT 2015] net.sf.picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/gscuser/iferguso/links/check-illumina-dir-example/Data/Intensities/BaseCalls READ_STRUCTURE=151T6B LANES=[1] TMP_DIR=[/tmp/gm-genome_sys-2015-04-02_15_54_06--uKe5/Picard-FXPp] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=500000    FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false\r\n[Thu Apr 02 15:54:06 CDT 2015] Executing as iferguso@linus47.gsc.wustl.edu on Linux 2.6.35-31-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_18-b07; Picard version: 1.113(exported) JdkDeflater\r\nINFO    2015-04-02 15:54:06     CheckIlluminaDirectory  Checking lanes(1 in basecalls directory (/gscuser/iferguso/links/check-illumina-dir-example/Data/Intensities/BaseCalls)\r\n\r\nINFO    2015-04-02 15:54:06     CheckIlluminaDirectory  Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157\r\nINFO    2015-04-02 15:54:06     CheckIlluminaDirectory  Checking lane 1\r\nINFO    2015-04-02 15:54:06     CheckIlluminaDirectory  Expected tiles: 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109, 2110, 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119\r\nINFO    2015-04-02 15:54:08     CheckIlluminaDirectory  Lane 1 SUCCEEDED\r\nINFO    2015-04-02 15:54:08     CheckIlluminaDirectory  SUCCEEDED!  All required files are present and non-empty.\r\n[Thu Apr 02 15:54:08 CDT 2015] net.sf.picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.04 minutes.\r\nRuntime.totalMemory()=93913088\r\n```\r\n\r\nWe believe that data is probably PHI. It's not immediately clear how to generate fake test data that's significantly smaller (both in size and number of files... there are thousands of files in the `BaseCalls` 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