115 lines
4.2 KiB
C
115 lines
4.2 KiB
C
/*
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Description: read ends结构体主要用来标记冗余，包含一些序列的测序过程中的物理信息等
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2023/11/3
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*/
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#ifndef READ_ENDS_H_
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#define READ_ENDS_H_
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#include <stdint.h>
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/**
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* Small interface that provides access to the physical location information about a cluster.
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* All values should be defaulted to -1 if unavailable. ReadGroup and Tile should only allow
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* non-zero positive integers, x and y coordinates may be negative.
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*/
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struct PhysicalLocation
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{
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/**
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* Small class that provides access to the physical location information about a cluster.
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* All values should be defaulted to -1 if unavailable. Tile should only allow
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* non-zero positive integers, x and y coordinates must be non-negative.
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* This is different from PhysicalLocationShort in that the x and y positions are ints, not shorts
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* thus, they do not overflow within a HiSeqX tile.
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*/
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int16_t tile = -1;
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int32_t x = -1;
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int32_t y = -1;
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};
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/* 包含了所有read ends信息，如picard里边的 ReadEndsForMarkDuplicates*/
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struct ReadEnds : PhysicalLocation
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{
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/* ReadEnds中的成员变量 */
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/** Little struct-like class to hold read pair (and fragment) end data for duplicate marking. */
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static const int8_t F = 0, R = 1, FF = 2, FR = 3, RR = 4, RF = 5;
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// int16_t libraryId; // 没用，不考虑多样本
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int8_t orientation;
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int32_t read1ReferenceIndex = -1;
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int32_t read1Coordinate = -1;
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int32_t read2ReferenceIndex = -1;
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int32_t read2Coordinate = -1; // This field is overloaded for flow based processing as the end coordinate of read 1. (paired reads not supported)
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/* Additional information used to detect optical dupes */
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// int16_t readGroup = -1; 一般经过比对后的bam文件只有一个read group，normal或者tumor
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/** For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate */
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int8_t orientationForOpticalDuplicates = -1;
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/** A *transient* flag marking this read end as being an optical duplicate. */
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bool isOpticalDuplicate = false;
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/* ReadEndsForMarkDuplicates中的成员变量 */
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/** Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar **/
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int16_t score = 0;
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int64_t read1IndexInFile = -1;
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int64_t read2IndexInFile = -1;
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int64_t duplicateSetSize = -1;
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/* ReadEndsForMarkDuplicatesWithBarcodes中的成员变量 (好像用不到) */
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// int32_t barcode = 0; // primary barcode for this read (and pair)
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// int32_t readOneBarcode = 0; // read one barcode, 0 if not present
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// int32_t readTwoBarcode = 0; // read two barcode, 0 if not present or not paired
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/* zzh增加的成员变量 */
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int64_t posKey = -1; // 根据位置信息生成的关键字 return (int64_t)tid << MAX_CONTIG_LEN_SHIFT | (int64_t)pos;
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/* 根据pairend read的比对方向，来确定整体的比对方向 */
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static int8_t GetOrientationByte(bool read1NegativeStrand, bool read2NegativeStrand)
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{
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if (read1NegativeStrand)
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{
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if (read2NegativeStrand)
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return RR;
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else
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return RF;
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}
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else
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{
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if (read2NegativeStrand)
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return FR;
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else
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return FF;
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}
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}
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/* 比较两个readends是否一样（有个冗余） */
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static bool AreComparableForDuplicates(ReadEnds &lhs, ReadEnds &rhs, bool compareRead2)
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{
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bool areComparable = true;
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areComparable = lhs.read1ReferenceIndex == rhs.read1ReferenceIndex &&
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lhs.read1Coordinate == rhs.read1Coordinate &&
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lhs.orientation == rhs.orientation;
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if (areComparable && compareRead2)
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{
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areComparable = lhs.read2ReferenceIndex == rhs.read2ReferenceIndex &&
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lhs.read2Coordinate == rhs.read2Coordinate;
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}
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return areComparable;
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}
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/* 比对方向是否正向 */
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bool IsForwardStrand()
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{
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return orientation == F;
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}
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/* pairend是否合适的比对上了 */
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bool IsPaired()
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{
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return read2ReferenceIndex != -1;
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}
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};
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#endif |