FastqToUnmappedSam

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1. final def !=(arg0: Any): Boolean

   

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2. final def ##(): Int

   

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3. final def ==(arg0: Any): Boolean

   

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4. def apply(fq1: PathToFastq, fq2: PathToFastq, bam: PathToBam, sm: String, lb: String, pu: String, rgId: Option[String] = None, prefix: Option[Path], qualityFormat: Option[FastqQualityFormat] = None): Pipe[Nothing, SamOrBam]

   

   Constructs a new set of piped tasks for taking PE Illumina data from two fastq files and producing an unampped BAM file in which the possible location of adapter sequence in each read is marked.

   Constructs a new set of piped tasks for taking PE Illumina data from two fastq files and producing an unampped BAM file in which the possible location of adapter sequence in each read is marked.

   fq1

   the read one fastq file (can be gzipped)

   fq2

   the read two fastq file (can be gzipped)

   bam

   the output SAM or BAM file to write to

   sm

   the name of the sample to put in the read group header

   lb

   the name of the library to put in the read group header

   pu

   the platform unit string to put in the tread group header

   rgId

   the optional ID to use in the read group header. If None one will be generated.

   prefix

   the prefix (including directories) to use to write metrics and ancillary files

   returns

   a Pipe from Nothing (since the inputs are read from file) to SamOrBam

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7. final def eq(arg0: AnyRef): Boolean

   

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8. def equals(arg0: Any): Boolean

   

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9. def finalize(): Unit

   

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