73 lines
2.6 KiB
Java
73 lines
2.6 KiB
Java
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package net.sf.samtools.util;
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import java.io.IOException;
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/**
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* An input stream formulated for use reading BAM files. Supports
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*/
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public interface BAMInputStream {
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/**
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* Seek to the given position in the file. Note that pos is a special virtual file pointer,
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* not an actual byte offset.
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*
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* @param pos virtual file pointer
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*/
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public void seek(final long pos) throws IOException;
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/**
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* @return virtual file pointer that can be passed to seek() to return to the current position. This is
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* not an actual byte offset, so arithmetic on file pointers cannot be done to determine the distance between
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* the two.
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*/
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public long getFilePointer();
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/**
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* Determines whether or not the inflater will re-calculated the CRC on the decompressed data
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* and check it against the value stored in the GZIP header. CRC checking is an expensive
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* operation and should be used accordingly.
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*/
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public void setCheckCrcs(final boolean check);
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public int read() throws java.io.IOException;
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public int read(byte[] bytes) throws java.io.IOException;
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public int read(byte[] bytes, int i, int i1) throws java.io.IOException;
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public long skip(long l) throws java.io.IOException;
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public int available() throws java.io.IOException;
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public void close() throws java.io.IOException;
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public void mark(int i);
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public void reset() throws java.io.IOException;
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public boolean markSupported();
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}
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