FastqScreenSAMParser (Aozan 3.1 API)

java.lang.Object
- fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenSAMParser

```
public class FastqScreenSAMParser
extends Object
```
This class ensures alignment fastqScreen treating the output format BAM of mapper.

Since:

1.0

Author:

Sandrine Perrin

Constructor Summary

Constructors
Constructor	Description
`FastqScreenSAMParser(File mapOutputFile, String genome, boolean pairedMode, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDescription)`	Initialize FastqScreenSAMParser : create the mapOutputFile and the list filters used for parsing SAM file.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getReadsprocessed()`
`void`	`parseLines(InputStream is)`	Parse a SAM file and create a new file mapoutsamfile, it contains a line for each read mapped with her name and mapping data : first character represent the number of hits for a read : 1 or 2 (for several hits) and the end represent the name of reference genome.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - FastqScreenSAMParser
```
public FastqScreenSAMParser(File mapOutputFile,
                            String genome,
                            boolean pairedMode,
                            fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDescription)
                     throws IOException
```
    Initialize FastqScreenSAMParser : create the mapOutputFile and the list filters used for parsing SAM file.
    
    Parameters:
    
    mapOutputFile - file result from mapping
    
    genome - name genome
    
    genomeDescription - description of the genome
    
    pairedMode - true if a pair-end run and option paired mode equals true else false
    
    Throws:
    
    IOException - if an error occurs while initializing mapOutputFile
- Method Detail
  - parseLines
```
public void parseLines(InputStream is)
                throws IOException
```
    Parse a SAM file and create a new file mapoutsamfile, it contains a line for each read mapped with her name and mapping data : first character represent the number of hits for a read : 1 or 2 (for several hits) and the end represent the name of reference genome.
    
    Parameters:
    
    is - inputStream to parse
    
    Throws:
    
    IOException
  - getReadsprocessed
```
public int getReadsprocessed()
```