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embed samtools sources directly, since Rsamtools has moved to htslib

Michael Lawrence authored on 11/02/2019 20:33:07
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+#ifndef BAM_ENDIAN_H
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+#define BAM_ENDIAN_H
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+
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+#include <stdint.h>
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+
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+static inline int bam_is_big_endian()
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+{
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+	long one= 1;
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+	return !(*((char *)(&one)));
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+}
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+static inline uint16_t bam_swap_endian_2(uint16_t v)
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+{
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+	return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
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+}
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+static inline void *bam_swap_endian_2p(void *x)
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+{
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+	*(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
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+	return x;
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+}
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+static inline uint32_t bam_swap_endian_4(uint32_t v)
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+{
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+	v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
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+	return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
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+}
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+static inline void *bam_swap_endian_4p(void *x)
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+{
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+	*(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
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+	return x;
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+}
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+static inline uint64_t bam_swap_endian_8(uint64_t v)
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+{
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+	v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
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+	v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
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+	return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
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+}
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+static inline void *bam_swap_endian_8p(void *x)
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+{
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+	*(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
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+	return x;
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+}
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+
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+#endif