From 19e27d4568c56246f335118a4accac2ec005dd29 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 27 Oct 2011 23:55:11 -0400
Subject: [PATCH] Removing all instances of -BTI (in tests and in GATKdocs) and
 replacing them with the appropriate alternative.

---
 .../phasing/ReadBackedPhasingWalker.java      |  5 ++--
 .../validation/GenotypeAndValidateWalker.java |  6 ++--
 .../validation/ValidationAmplicons.java       |  2 +-
 .../sting/utils/interval/IntervalUtils.java   |  2 +-
 .../VariantAnnotatorIntegrationTest.java      | 12 ++++----
 ...RealignerTargetCreatorIntegrationTest.java |  2 +-
 .../ValidationAmpliconsIntegrationTest.java   |  6 ++--
 .../VariantEvalIntegrationTest.java           | 30 +++++++++----------
 .../utils/codecs/vcf/VCFIntegrationTest.java  |  2 +-
 9 files changed, 33 insertions(+), 34 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 998cfa654..2c2677d82 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -75,9 +75,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
  *      -T ReadBackedPhasing
  *      -R reference.fasta
  *      -I reads.bam
- *      --variant:vcf SNPs.vcf
- *      -BTI variant
- *      -BTIMR INTERSECTION
+ *      --variant SNPs.vcf
+ *      -L SNPs.vcf
  *      -o phased_SNPs.vcf
  *      --phaseQualityThresh 20.0
  * </pre>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
index c2f6e2099..fd55d78a0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -141,7 +141,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
  *  <h3>Additional Details</h3>
  *  <ul>
  *      <li>
- *          You should always use -BTI on your VCF track, so that the GATK only looks at the sites on the VCF file.
+ *          You should always use -L on your VCF track, so that the GATK only looks at the sites on the VCF file.
  *          This speeds up the process a lot.
  *      </li>
  *      <li>
@@ -164,7 +164,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
  *      -R human_g1k_v37.fasta
  *      -I myNewTechReads.bam
  *      -alleles handAnnotatedVCF.vcf
- *      -BTI alleles
+ *      -L handAnnotatedVCF.vcf
  * </pre>
  *
  *      <li>
@@ -178,7 +178,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
  *      -R human_g1k_v37.fasta
  *      -I myTruthDataset.bam
  *      -alleles callsToValidate.vcf
- *      -BTI alleles
+ *      -L callsToValidate.vcf
  *      -bt
  *      -o gav.vcf
  * </pre>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index 48cba6a1a..035d8d2ca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -80,7 +80,7 @@ import java.util.List;
  *      -jar GenomeAnalysisTK.jar
  *      -T ValidationAmplicons
  *      -R /humgen/1kg/reference/human_g1k_v37.fasta
- *      -BTI ProbeIntervals
+ *      -L:table interval_table.table
  *      -ProbeIntervals:table interval_table.table
  *      -ValidateAlleles:vcf sites_to_validate.vcf
  *      -MaskAlleles:vcf mask_sites.vcf
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index 2e191511b..139cded37 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -196,7 +196,7 @@ public class IntervalUtils {
 
         //if we have an empty list, throw an exception.  If they specified intersection and there are no items, this is bad.
         if (retList.size() == 0)
-                throw new UserException.BadInput("The INTERSECTION of your -BTI and -L options produced no intervals.");
+                throw new UserException.BadInput("The INTERSECTION of your -L options produced no intervals.");
 
         // we don't need to add the rest of remaining locations, since we know they don't overlap. return what we have
         return retList;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 2fed668c5..2b963967d 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
+                baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
                 Arrays.asList("78d2c19f8107d865970dbaf3e12edd92"));
         executeTest("test overwriting header", spec);
     }
@@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
                 Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
         executeTest("not passing it any reads", spec);
     }
@@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --dbsnp " + b36dbSNP129 + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
                 Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
         executeTest("getting DB tag with dbSNP", spec);
     }
@@ -111,7 +111,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
                 Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
         executeTest("getting DB tag with HM3", spec);
     }
@@ -119,7 +119,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
+                baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
                 Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
         executeTest("using expression", spec);
     }
@@ -129,7 +129,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
-                    baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + file + " -BTI variant -NO_HEADER", 1,
+                    baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf -NO_HEADER", 1,
                     Arrays.asList(MD5));
             executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
         }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
index 78b24d646..26e23e016 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
@@ -44,7 +44,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
     @Test
     public void testKnownsOnly() {
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -R " + b36KGReference + " --known " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI known -o %s",
+                "-T RealignerTargetCreator -R " + b36KGReference + " --known " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s",
                  1,
                  Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96"));
         executeTest("test rods only", spec3);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
index 0a0d8c5b2..155d3c4db 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
@@ -20,7 +20,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
         String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
         String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
-        testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
+        testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("27f9450afa132888a8994167f0035fd7"));
@@ -33,7 +33,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
         String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
         String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
-        testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
+        testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30 --doNotUseBWA";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("f2611ff1d9cd5bedaad003251fed8bc1"));
@@ -46,7 +46,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
         String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
         String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
-        testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
+        testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30 --filterMonomorphic";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("77b3f30e38fedad812125bdf6cf3255f"));
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 9fe253ecb..cd2493dde 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -26,7 +26,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-EV TiTvVariantEvaluator",
                                         "-noST",
                                         "-ST FunctionalClass",
-                                        "-BTI eval",
+                                        "-L " + validationDataLocation + "snpEff.AFR.unfiltered.VariantAnnotator.output.vcf",
                                         "-o %s"
                                 ),
                                 1,
@@ -46,7 +46,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-noEV",
                                         "-EV TiTvVariantEvaluator",
                                         "-ST Sample",
-                                        "-BTI eval",
+                                        "-L " + variantEvalTestDataRoot + "/CEU.trio.callsForVE.vcf",
                                         "-o %s"
                                 ),
                                 1,
@@ -66,7 +66,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-noEV",
                                         "-EV CountVariants",
                                         "-noST",
-                                        "-BTI eval",
+                                        "-L " + fundamentalTestVCF,
                                         "-o %s"
                                 ),
                                 1,
@@ -87,7 +87,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-EV CountVariants",
                         "-noST",
                         "-ST Novelty",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -109,7 +109,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-noST",
                         "-ST Novelty",
                         "-ST Filter",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -130,7 +130,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-EV CountVariants",
                         "-noST",
                         "-ST CpG",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -151,7 +151,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-EV CountVariants",
                         "-noST",
                         "-ST FunctionalClass",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -172,7 +172,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-EV CountVariants",
                         "-noST",
                         "-ST Degeneracy",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -193,7 +193,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-EV CountVariants",
                         "-noST",
                         "-ST Sample",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -216,7 +216,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-ST JexlExpression",
                         "-select 'DP < 20'",
                         "-selectName DepthSelect",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -241,7 +241,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-selectName DepthLt20",
                         "-select 'DP > 20'",
                         "-selectName DepthGt20",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -260,7 +260,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-noEV",
                         "-EV CountVariants",
                         "-noST",
-                        "-BTI eval",
+                        "-L " + fundamentalTestVCF,
                         "-o %s"
                 ),
                 1,
@@ -371,7 +371,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-EV CompOverlap",
                         "-sn HG00625",
                         "-noST",
-                        "-BTI eval",
+                        "-L " + fundamentalTestSNPsVCF,
                         "-o %s"
                 ),
                 1,
@@ -388,7 +388,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-noEV",
                         "-EV CompOverlap",
                         "-noST",
-                        "-BTI eval",
+                        "-L " + fundamentalTestSNPsOneSampleVCF,
                         "-o %s"
                 ),
                 1,
@@ -410,7 +410,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-EV CountVariants",
                                         "-noST",
                                         "-ST AlleleCount",
-                                        "-BTI eval",
+                                        "-L " + fundamentalTestSNPsVCF,
                                         "-o %s"
                                 ),
                                 1,
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
index 2ef116708..c8a0c0ed6 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
@@ -17,7 +17,7 @@ public class VCFIntegrationTest extends WalkerTest {
 
         String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
 
-        String test1 = baseCommand + "-T VariantAnnotator --variant " + testVCF + " -BTI variant";
+        String test1 = baseCommand + "-T VariantAnnotator --variant " + testVCF + " -L " + testVCF;
         WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
         List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();