34 lines
789 B
C
34 lines
789 B
C
#pragma once
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#include <htslib/sam.h>
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#include <stdio.h>
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#include "sort.h"
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// Struct which contains the sorting key for TemplateCoordinate sort.
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struct TemplateCoordinateKey {
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int tid1;
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int tid2;
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hts_pos_t pos1;
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hts_pos_t pos2;
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bool neg1;
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bool neg2;
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const char *library;
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char *mid;
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char *name;
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bool is_upper_of_pair;
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};
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// Struct which contains the a record, and the pointer to the sort tag (if any) or
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// a combined ref / position / strand.
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// Used to speed up sorts (coordinate, by-tag, and template-coordinate).
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struct BamSortTag {
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bam1_t *bam_record;
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union {
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const uint8_t *tag;
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uint8_t pos_tid[12];
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TemplateCoordinateKey *key;
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} u;
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};
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int ks_radixsort(size_t n, OneBam* buf, const sam_hdr_t* h, int tid); |