From cac98ba5efbd3e354c0f7fb1f14a8eb2234603e6 Mon Sep 17 00:00:00 2001 From: aaron Date: Wed, 12 May 2010 17:40:27 +0000 Subject: [PATCH] a couple of small documentation fixes git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/coverage/CallableLociWalker.java | 6 +++--- .../gatk/walkers/coverage/CompareCallableLociWalker.java | 6 +++--- .../sting/gatk/walkers/qc/ReadClippingStatsWalker.java | 6 +++--- .../gatk/walkers/validation/RodSystemValidationWalker.java | 2 +- .../tracks/builders/TribbleRMDTrackBuilderUnitTest.java | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java index 3fbfa0bbf..633f3ca12 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java @@ -2,15 +2,15 @@ * Copyright (c) 2009 The Broad Institute * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation - * Þles (the ÓSoftwareÓ), to deal in the Software without + * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, sub ject to the following + * Software is furnished to do so, subject to the following * conditions: * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. - * THE SOFTWARE IS PROVIDED ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND, + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java index d588ab0eb..194e96803 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java @@ -2,15 +2,15 @@ * Copyright (c) 2009 The Broad Institute * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation - * Þles (the ÓSoftwareÓ), to deal in the Software without + * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, sub ject to the following + * Software is furnished to do so, subject to the following * conditions: * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. - * THE SOFTWARE IS PROVIDED ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND, + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java index 41253e7f9..4f8d6e49f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java @@ -2,15 +2,15 @@ * Copyright (c) 2009 The Broad Institute * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation - * Þles (the ÓSoftwareÓ), to deal in the Software without + * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, sub ject to the following + * Software is furnished to do so, subject to the following * conditions: * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. - * THE SOFTWARE IS PROVIDED ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND, + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java index 76a3e0a48..408befb0d 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java @@ -97,7 +97,7 @@ public class RodSystemValidationWalker extends RodWalker { try { is = new FileInputStream(f); } catch (FileNotFoundException e) { - throw new StingException("Unable to get a file input stream from " + f, e); + return "Not a file"; } byte[] buffer = new byte[8192]; int read = 0; diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java index b02026880..0c99bd9f2 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java @@ -41,7 +41,7 @@ import java.util.Map; * * Class TribbleRMDTrackBuilderUnitTest * - * Testing out the builder for tribble Tracks (not really a functional test right now) + * Testing out the builder for tribble Tracks */ public class TribbleRMDTrackBuilderUnitTest extends BaseTest { private TribbleRMDTrackBuilder builder;