Package org.snpeff.vcf
Class FileIndexChrPos
java.lang.Object
org.snpeff.vcf.FileIndexChrPos
Index a file that has "chr \t pos" as the beginning of a line (e.g. VCF)
WARNING: It is assumed that the file is ordered by position (chromosome order does not matter)
- Author:
- pcingola
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionclass
A part of a fileclass
A line and the position on the file where it begins -
Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Close fileDump all lines in the interval chr:posStart-posEndlong
Find the position in the file for the first character of the first line equal or less than a specific chr:posbyte
get
(long bytePosition) Get a byte from a filebyte[]
get
(long bytePosition, int len) Read 'len' bytes after 'bytePosition' or until a '\n' is reached.Available chromosomeslong
Get position where 'chr' endsgetLine
(long pos) Get the line where 'pos' hitsgetLineSlow
(long pos) A slow method for getLinelong
Get position where 'chr' startsvoid
index()
Index chromosomes in the whole filevoid
open()
Open file and initiate mappingsint
The position argument of a line (second column in tab-separated format).void
setDebug
(boolean debug) void
setVerbose
(boolean verbose) long
size()
File sizetoString()
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Field Details
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POS_OFFSET
public static final int POS_OFFSET- See Also:
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Constructor Details
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FileIndexChrPos
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Method Details
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close
public void close()Close file -
dump
Dump all lines in the interval chr:posStart-posEnd- Parameters:
chr
- : ChromosomeposStart
- : Start coordinate in chromosome (zero-based)posEnd
- : End coordinate in chromosome (zero-based)toString
- : Return a sting with file contents?- Returns:
- If toString is 'true', return a string with file's content between those coordinates (this is used only for test cases and debugging)
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find
Find the position in the file for the first character of the first line equal or less than a specific chr:pos -
get
public byte get(long bytePosition) Get a byte from a file -
get
public byte[] get(long bytePosition, int len) Read 'len' bytes after 'bytePosition' or until a '\n' is reached. If len is negative, read 'abs(len)' bytes before bytePosition or until '\n' is reached- Parameters:
bytePosition
-len
-- Returns:
- An array of 'len' bytes. null if either end of file (len > 0) or beginning of file (len invalid input: '<' 0)
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getChromos
Available chromosomes- Returns:
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getEnd
Get position where 'chr' ends- Parameters:
chr
-- Returns:
- -1 if 'chr' is not in the index
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getLine
Get the line where 'pos' hits- Returns:
- A string with the line that 'pos' hits, null if it's out of boundaries
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getLineSlow
A slow method for getLine -
getStart
Get position where 'chr' starts- Parameters:
chr
-- Returns:
- -1 if 'chr' is not in the index
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index
public void index()Index chromosomes in the whole file -
open
public void open()Open file and initiate mappings -
pos
The position argument of a line (second column in tab-separated format). Negative if not found- Returns:
- The position argument of a line. Negative if not found
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setDebug
public void setDebug(boolean debug) -
setVerbose
public void setVerbose(boolean verbose) -
size
public long size()File size -
toString
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