From eb9709793ab6eaa2ac573346d3f216a8f2891de2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daniel=20G=C3=B3mez-S=C3=A1nchez?= Date: Wed, 25 Jan 2017 15:59:17 +0100 Subject: [PATCH] Add getters for defaults SAMFileWriterFactory fields --- src/main/java/htsjdk/samtools/SAMFileWriterFactory.java | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/src/main/java/htsjdk/samtools/SAMFileWriterFactory.java b/src/main/java/htsjdk/samtools/SAMFileWriterFactory.java index 61f1c9c13..b788fbe89 100644 --- a/src/main/java/htsjdk/samtools/SAMFileWriterFactory.java +++ b/src/main/java/htsjdk/samtools/SAMFileWriterFactory.java @@ -86,6 +86,14 @@ public static void setDefaultCreateMd5File(final boolean createMd5File) { } /** + * Gets the default for whether to create md5Files for BAM files this factory. + * @see #setDefaultCreateMd5File(boolean) + */ + public static boolean getDefaultCreateMd5File() { + return defaultCreateMd5File; + } + + /** * Sets whether to create md5Files for BAMs from this factory. */ public SAMFileWriterFactory setCreateMd5File(final boolean createMd5File) { @@ -128,6 +136,14 @@ public static void setDefaultCreateIndexWhileWriting(final boolean setting) { } /** + * Gets the default for subsequent SAMFileWriterFactories that do not specify whether to create an index. + * @see #setDefaultCreateIndexWhileWriting + */ + public static boolean getDefaultCreateIndexWhileWriting() { + return defaultCreateIndexWhileWriting; + } + + /** * Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true); * Equivalent to SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true); newSAMFileWriterFactory(); * If a BAM or CRAM (not SAM) file is created, the setting is true, and the file header specifies coordinate order,