{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/66142118","id":66142118,"diff_hunk":"@@ -0,0 +1,226 @@\n+package org.broadinstitute.hellbender.tools.walkers.qc;\n+\n+import org.broadinstitute.hellbender.cmdline.Argument;\n+import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;\n+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;\n+import org.broadinstitute.hellbender.cmdline.programgroups.QCProgramGroup;\n+import org.broadinstitute.hellbender.engine.*;\n+import org.broadinstitute.hellbender.exceptions.GATKException;\n+import org.broadinstitute.hellbender.exceptions.UserException;\n+import org.broadinstitute.hellbender.utils.IntervalUtils;\n+import org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature;\n+import org.broadinstitute.hellbender.utils.pileup.ReadPileup;\n+\n+import java.io.PrintStream;\n+import java.util.Arrays;\n+import java.util.List;\n+\n+/**\n+ * Compare GATK's internal pileup to a reference Samtools pileup\n+ *\n+ * <p>At every locus in the input set, compares the pileup data (reference base, aligned base from\n+ * each overlapping read, and quality score) generated internally by GATK to a reference pileup data generated\n+ * by Samtools. Note that the pileup program has been replaced in Samtools by mpileup, which produces a slightly\n+ * different output format by default.\n+ * </p>\n+ *\n+ * <h3>Format</h3>\n+ * <p>There are two versions of the original pileup format: the current 6-column format produced by Samtools, and the old\n+ * 10-column \"consensus\" format which could be obtained by using the -c argument, now deprecated.</p>\n+ * <h4>Simple pileup: 6-column format</h4>\n+ * <p>\n+ *     Each line consists of chromosome, 1-based coordinate, reference base, the\n+ *     number of reads covering the site, read bases and base qualities. At the\n+ *     read base column, a dot stands for a match to the reference base on the\n+ *     forward strand, a comma for a match on the reverse strand, `ACGTN' for a mismatch\n+ *     on the forward strand and `acgtn' for a mismatch on the reverse strand.\n+ *     A pattern `\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between\n+ *     this reference position and the next reference position. The length of the\n+ *     insertion is given by the integer in the pattern, followed by the inserted sequence.\n+ * </p>\n+ * <pre>\n+ *     seq1 272 T 24  ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&\n+ *     seq1 273 T 23  ,.....,,.,.,...,,,.,..A <<<;<<<<<<<<<3<=<<<;<<+\n+ *     seq1 274 T 23  ,.$....,,.,.,...,,,.,...    7<7;<;<<<<<<<<<=<;<;<<6\n+ *     seq1 275 A 23  ,$....,,.,.,...,,,.,...^l.  <+;9*<<<<<<<<<=<<:;<<<<\n+ *     seq1 276 G 22  ...T,,.,.,...,,,.,....  33;+<<7=7<<7<&<<1;<<6<\n+ *     seq1 277 T 22  ....,,.,.,.C.,,,.,..G.  +7<;<<<<<<<&<=<<:;<<&<\n+ *     seq1 278 G 23  ....,,.,.,...,,,.,....^k.   %38*<<;<7<<7<=<<<;<<<<<\n+ *     seq1 279 C 23  A..T,,.,.,...,,,.,..... ;75&<<<<<<<<<=<<<9<<:<<\n+ * </pre>\n+ * <p>\n+ *     See the <a href=\"http://samtools.sourceforge.net/pileup.shtml\">Pileup format documentation</a> for more details.\n+ * </p>\n+ *\n+ * <h4>Consensus pileup: 10/13-column format</h4>\n+ * <p>The \"consensus\" or extended pileup consists of the following:\n+ *  <ul>\n+ *      <li>original 6 columns as described above</li>\n+ *      <li>4 extra columns representing consensus values (consensus base, consensus quality, variant quality and maximum mapping quality of the\n+ * reads covering the sites) for all sites, inserted before the bases and quality strings</li>\n+ *      <li>3 extra columns indicating counts of reads supporting indels (just for indel sites)</li>\n+ *  </ul>\n+ * </p>\n+ * <h4>Example of consensus pileup for SNP or non-variant sites</h4>\n+ * <pre>\n+ *     seq1  60  T  T  66  0  99  13  ...........^~.^~.   9<<55<;<<<<<<\n+ *     seq1  61  G  G  72  0  99  15  .............^~.^y. (;975&;<<<<<<<<\n+ *     seq1  62  T  T  72  0  99  15  .$..............    <;;,55;<<<<<<<<\n+ *     seq1  63  G  G  72  0  99  15  .$.............^~.  4;2;<7:+<<<<<<<\n+ *     seq1  64  G  G  69  0  99  14  ..............  9+5<;;;<<<<<<<\n+ *     seq1  65  A  A  69  0  99  14  .$............. <5-2<;;<<<<<<;\n+ *     seq1  66  C  C  66  0  99  13  .............   &*<;;<<<<<<8<\n+ *     seq1  67  C  C  69  0  99  14  .............^~.    ,75<.4<<<<<-<<\n+ *     seq1  68  C  C  69  0  99  14  ..............  576<;7<<<<<8<< *\n+ * </pre>\n+ *\n+ * <h4>Example of consensus pileup for indels</h4>\n+ * <pre>\n+ *     Escherichia_coli_K12\t3995037\t*\t*\\/*\t430\t0\t37\t144\t*\t+A\t143\t1\t0\n+ *     Escherichia_coli_K12\t3995279\t*\t*\\/*\t202\t0\t36\t68\t*\t+A\t67\t1\t0\n+ *     Escherichia_coli_K12\t3995281\t*\t*\\/*\t239\t0\t36\t67\t*\t-CG\t66\t1\t0\n+ * </pre>\n+ * <p>\n+ *     See <a href=\"http://samtools.sourceforge.net/cns0.shtml/\">Consensus pileup format (deprecated)</a> for more details.\n+ * </p>\n+ *\n+ * <h3>Input</h3>\n+ * <p>A BAM file containing your aligned sequence data and a pileup file generated by Samtools covering the region you\n+ * want to examine.</p>\n+ *\n+ * <h3>Output</h3>\n+ * <p>A text file listing mismatches between the input pileup and the GATK's internal pileup. If there are no mismatches, the output file is empty.</p>\n+ *\n+ * <h3>Usage example</h3>\n+ * <pre>\n+ * ./gatk-launch CheckPileup \\\n+ *   -R reference.fasta \\\n+ *   -I your_data.bam \\\n+ *   --pileup pileup_file.txt \\\n+ *   -L chr1:257-275 \\\n+ *   -O output_file_name\n+ * </pre>\n+ */\n+@CommandLineProgramProperties(\n+    summary = \"At every locus in the input set, compares the pileup data (reference base, aligned base from each overlapping\"\n+        + \"read, and quality score) generated internally by GATK to a reference pileup data generated by Samtools. Note \"\n+        + \"that the pileup program has been replaced in Samtools by mpileup, which produces a slightly different output \"\n+        + \"format by default.\",\n+    oneLineSummary = \"Compare GATK's internal pileup to a reference Samtools pileup\",\n+    programGroup = QCProgramGroup.class)\n+public class CheckPileup extends LocusWalker {\n+\n+    /**\n+     * This is the existing pileup against which we'll compare GATK's internal pileup at each genome position in the desired interval.\n+     */\n+    @Argument(fullName = \"pileup\", shortName = \"pileup\", doc=\"Pileup generated by Samtools\")\n+    FeatureInput<SAMPileupFeature> pileup;\n+\n+    @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = \"An output file created by the walker. Will overwrite contents if file exists\")\n+    private PrintStream out;\n+    /**\n+     * By default the program will quit if it encounters an error (such as missing truth data for a given position).\n+     * Use this flag to override the default behavior; the program will then simply print an error message and move on\n+     * to the next position.\n+     */\n+    @Argument(fullName=\"continue_after_error\",doc=\"Continue after encountering an error\",optional=true)\n+    public boolean continueAfterAnError = false;\n+\n+    @Override\n+    public boolean requiresReference() {\n+        return true;\n+    }\n+\n+    public long nLoci = 0;","path":"src/main/java/org/broadinstitute/hellbender/tools/walkers/qc/CheckPileup.java","position":134,"original_position":134,"commit_id":"9b494818d2131cd4617c8398737fc4e7fd2681b2","original_commit_id":"9b494818d2131cd4617c8398737fc4e7fd2681b2","user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"body":"these should probably be private","created_at":"2016-06-07T20:04:07Z","updated_at":"2016-06-07T20:04:07Z","html_url":"https://github.com/broadinstitute/gatk/pull/1862#discussion_r66142118","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1862","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/66142118"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1862#discussion_r66142118"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1862"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1862","id":71702403,"html_url":"https://github.com/broadinstitute/gatk/pull/1862","diff_url":"https://github.com/broadinstitute/gatk/pull/1862.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1862.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1862","number":1862,"state":"open","locked":false,"title":"Port CheckPileup","user":{"login":"magicDGS","id":7352559,"avatar_url":"https://avatars.githubusercontent.com/u/7352559?v=3","gravatar_id":"","url":"https://api.github.com/users/magicDGS","html_url":"https://github.com/magicDGS","followers_url":"https://api.github.com/users/magicDGS/followers","following_url":"https://api.github.com/users/magicDGS/following{/other_user}","gists_url":"https://api.github.com/users/magicDGS/gists{/gist_id}","starred_url":"https://api.github.com/users/magicDGS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/magicDGS/subscriptions","organizations_url":"https://api.github.com/users/magicDGS/orgs","repos_url":"https://api.github.com/users/magicDGS/repos","events_url":"https://api.github.com/users/magicDGS/events{/privacy}","received_events_url":"https://api.github.com/users/magicDGS/received_events","type":"User","site_admin":false},"body":"Because I'm implementing a program in GATK that comes for a pipeline using `samtools mpileup` and post-processing the file, I need a way to check if the internal `ReadPileup` generated by the tool is indeed the same as the one obtained for samtools.\r\n\r\nThus, I ported the `CheckPileup` tool from GATK3 in this PR.","created_at":"2016-05-27T12:02:42Z","updated_at":"2016-06-07T20:04:07Z","closed_at":null,"merged_at":null,"merge_commit_sha":"b43b85c1fa0c6df12e8d270bdda1a03119c864cc","assignee":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1862/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1862/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1862/comments","statuses_url":"https://api.github.com/repos/broadinstitute/gatk/statuses/9b494818d2131cd4617c8398737fc4e7fd2681b2","head":{"label":"magicDGS:dgs_check_pileup","ref":"dgs_check_pileup","sha":"9b494818d2131cd4617c8398737fc4e7fd2681b2","user":{"login":"magicDGS","id":7352559,"avatar_url":"https://avatars.githubusercontent.com/u/7352559?v=3","gravatar_id":"","url":"https://api.github.com/users/magicDGS","html_url":"https://github.com/magicDGS","followers_url":"https://api.github.com/users/magicDGS/followers","following_url":"https://api.github.com/users/magicDGS/following{/other_user}","gists_url":"https://api.github.com/users/magicDGS/gists{/gist_id}","starred_url":"https://api.github.com/users/magicDGS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/magicDGS/subscriptions","organizations_url":"https://api.github.com/users/magicDGS/orgs","repos_url":"https://api.github.com/users/magicDGS/repos","events_url":"https://api.github.com/users/magicDGS/events{/privacy}","received_events_url":"https://api.github.com/users/magicDGS/received_events","type":"User","site_admin":false},"repo":{"id":56243756,"name":"gatk","full_name":"magicDGS/gatk","owner":{"login":"magicDGS","id":7352559,"avatar_url":"https://avatars.githubusercontent.com/u/7352559?v=3","gravatar_id":"","url":"https://api.github.com/users/magicDGS","html_url":"https://github.com/magicDGS","followers_url":"https://api.github.com/users/magicDGS/followers","following_url":"https://api.github.com/users/magicDGS/following{/other_user}","gists_url":"https://api.github.com/users/magicDGS/gists{/gist_id}","starred_url":"https://api.github.com/users/magicDGS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/magicDGS/subscriptions","organizations_url":"https://api.github.com/users/magicDGS/orgs","repos_url":"https://api.github.com/users/magicDGS/repos","events_url":"https://api.github.com/users/magicDGS/events{/privacy}","received_events_url":"https://api.github.com/users/magicDGS/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/magicDGS/gatk","description":"GATK4 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