From 81c237a9ce72d892f72653b7a25a56dc0e78e59e Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Mon, 10 Jul 2017 14:40:38 -0400 Subject: [PATCH 1/2] - oops broke the old option EXPECT_ALL_READ_GROUPS_TO_MATCH. Sorry. --- .../java/picard/fingerprint/CrosscheckReadGroupFingerprints.java | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java index 6255f5c82..d88722306 100644 --- a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java +++ b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java @@ -60,6 +60,11 @@ "and print out a library x library matrix with LOD scores.") public boolean CROSSCHECK_LIBRARIES = false; + @Option(doc="Expect all read groups' fingerprints to match, irrespective of their sample names. By default (with this value set to " + + "false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected " + + "to match.", mutex = {"EXPECT_ALL_GROUPS_TO_MATCH"}) + public boolean EXPECT_ALL_READ_GROUPS_TO_MATCH = false; + @Override protected String[] customCommandLineValidation() { final List errors = new ArrayList<>(); @@ -86,6 +91,8 @@ @Override protected int doWork() { + if (EXPECT_ALL_READ_GROUPS_TO_MATCH) EXPECT_ALL_GROUPS_TO_MATCH = EXPECT_ALL_READ_GROUPS_TO_MATCH; + if (CROSSCHECK_LIBRARIES) { CROSSCHECK_BY = CrosscheckMetric.DataType.LIBRARY; } else if (CROSSCHECK_SAMPLES) { From 980206ca8dae6c65fa1080b308ae7eb6c7b1fd3e Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Tue, 11 Jul 2017 08:53:43 -0400 Subject: [PATCH 2/2] - review comments --- .../picard/fingerprint/CrosscheckReadGroupFingerprints.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java index d88722306..b314b7a64 100644 --- a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java +++ b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java @@ -38,16 +38,14 @@ * individual. * * @author Tim Fennell + * + * @deprecated 6/6/2017 Use {@link CrosscheckFingerprints} instead. */ @CommandLineProgramProperties( usage = "DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups within a set of BAM files appear to come from the same individual", usageShort = "DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups appear to come from the same individual.", programGroup = Fingerprinting.class ) -/** - @deprecated 6/6/2017 - Use {@link CrosscheckFingerprints} instead. - */ @Deprecated public class CrosscheckReadGroupFingerprints extends CrosscheckFingerprints { @@ -60,7 +58,7 @@ "and print out a library x library matrix with LOD scores.") public boolean CROSSCHECK_LIBRARIES = false; - @Option(doc="Expect all read groups' fingerprints to match, irrespective of their sample names. By default (with this value set to " + + @Option(doc = "Expect all read groups' fingerprints to match, irrespective of their sample names. By default (with this value set to " + "false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected " + "to match.", mutex = {"EXPECT_ALL_GROUPS_TO_MATCH"}) public boolean EXPECT_ALL_READ_GROUPS_TO_MATCH = false; @@ -91,7 +89,9 @@ @Override protected int doWork() { - if (EXPECT_ALL_READ_GROUPS_TO_MATCH) EXPECT_ALL_GROUPS_TO_MATCH = EXPECT_ALL_READ_GROUPS_TO_MATCH; + if (EXPECT_ALL_READ_GROUPS_TO_MATCH) { + EXPECT_ALL_GROUPS_TO_MATCH = EXPECT_ALL_READ_GROUPS_TO_MATCH; + } if (CROSSCHECK_LIBRARIES) { CROSSCHECK_BY = CrosscheckMetric.DataType.LIBRARY;