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a couple of small documentation fixes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-05-12 17:40:27 +00:00
parent 2a803e9044
commit cac98ba5ef
5 changed files with 11 additions and 11 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
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@ -2,15 +2,15 @@
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * 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, * restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell * copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the * 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: * conditions:
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * 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 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT

6
java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
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@ -2,15 +2,15 @@
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * 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, * restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell * copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the * 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: * conditions:
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * 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 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT

6
java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
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@ -2,15 +2,15 @@
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * 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, * restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell * copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the * 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: * conditions:
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * 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 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
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@ -97,7 +97,7 @@ public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
try { try {
is = new FileInputStream(f); is = new FileInputStream(f);
} catch (FileNotFoundException e) { } 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]; byte[] buffer = new byte[8192];
int read = 0; int read = 0;

2
java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java
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@ -41,7 +41,7 @@ import java.util.Map;
* *
* Class TribbleRMDTrackBuilderUnitTest * 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 { public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
private TribbleRMDTrackBuilder builder; private TribbleRMDTrackBuilder builder;