File: Enumerations.h

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// Author: Mark Chaisson

#ifndef _BLASR_ENUMERATIONS_HPP_
#define _BLASR_ENUMERATIONS_HPP_

enum class FileType
{
    Fasta,
    Fastq,
    HDFPulse,
    Fourbit,
    HDFBase,
    HDFCCS,
    HDFCCSONLY,
    PBBAM,
    PBDATASET,
    None
};

typedef enum T_Strand { Forward, Reverse } Strand;

typedef enum T_PlatformType { Astro = 1, Springfield = 2, Sequel = 4, NoPlatform } PlatformId;

typedef enum T_RegionType { Adapter, Insert, HQRegion, BarCode, UnknownRegionType } RegionType;

typedef enum T_PulseMetricType {
    QualityValueMetric,
    ClassifierQVMetric,
    StartTimeMetric,
    PulseWidthMetric,
    WidthInFramesMetric,
    pkmidMetric,
    IPDMetric,
    LightMetric,
    PreBaseFramesMetric
} PulseMetricType;

typedef enum T_AlignMode {
    NoAlignMode,
    Fullread,
    Subread,
    CCSDeNovo,
    CCSFullPass,
    CCSAllPass,
    ZmwSubreads
} AlignMode;

#endif