htslib/sam_internal.h at develop · SelfHacked/htslib · GitHub

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/* sam_internal.h -- internal functions; not part of the public API.

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER

DEALINGS IN THE SOFTWARE. */

#ifndef HTSLIB_SAM_INTERNAL_H

#define HTSLIB_SAM_INTERNAL_H

#include <errno.h>

#include <stdint.h>

#include "htslib/sam.h"

#ifdef __cplusplus

extern "C" {

#endif

// Used internally in the SAM format multi-threading.

int sam_state_destroy(samFile *fp);

int sam_set_thread_pool(htsFile *fp, htsThreadPool *p);

int sam_set_threads(htsFile *fp, int nthreads);

// bam1_t data (re)allocation

int sam_realloc_bam_data(bam1_t *b, size_t desired);

static inline int realloc_bam_data(bam1_t *b, size_t desired)

{

if (desired <= b->m_data) return 0;

return sam_realloc_bam_data(b, desired);

}

static inline int possibly_expand_bam_data(bam1_t *b, size_t bytes) {

size_t new_len = (size_t) b->l_data + bytes;

if (new_len > INT32_MAX || new_len < bytes) { // Too big or overflow

errno = ENOMEM;

return -1;

}

if (new_len <= b->m_data) return 0;

return sam_realloc_bam_data(b, new_len);

}

* Convert a nibble encoded BAM sequence to a string of bases.

* We do this 2 bp at a time for speed. Equiv to:

* for (i = 0; i < len; i++)

* seq[i] = seq_nt16_str[bam_seqi(nib, i)];

static inline void nibble2base(uint8_t *nib, char *seq, int len) {

static const char code2base[512] =

"===A=C=M=G=R=S=V=T=W=Y=H=K=D=B=N"

"A=AAACAMAGARASAVATAWAYAHAKADABAN"

"C=CACCCMCGCRCSCVCTCWCYCHCKCDCBCN"

"M=MAMCMMMGMRMSMVMTMWMYMHMKMDMBMN"

"G=GAGCGMGGGRGSGVGTGWGYGHGKGDGBGN"

"R=RARCRMRGRRRSRVRTRWRYRHRKRDRBRN"

"S=SASCSMSGSRSSSVSTSWSYSHSKSDSBSN"

"V=VAVCVMVGVRVSVVVTVWVYVHVKVDVBVN"

"T=TATCTMTGTRTSTVTTTWTYTHTKTDTBTN"

"W=WAWCWMWGWRWSWVWTWWWYWHWKWDWBWN"

"Y=YAYCYMYGYRYSYVYTYWYYYHYKYDYBYN"

"H=HAHCHMHGHRHSHVHTHWHYHHHKHDHBHN"

"K=KAKCKMKGKRKSKVKTKWKYKHKKKDKBKN"

"D=DADCDMDGDRDSDVDTDWDYDHDKDDDBDN"

"B=BABCBMBGBRBSBVBTBWBYBHBKBDBBBN"

"N=NANCNMNGNRNSNVNTNWNYNHNKNDNBNN";

int i, len2 = len/2;

seq[0] = 0;

for (i = 0; i < len2; i++)

// Note size_t cast helps gcc optimiser.

memcpy(&seq[i*2], &code2base[(size_t)nib[i]*2], 2);

if ((i *= 2) < len)

seq[i] = seq_nt16_str[bam_seqi(nib, i)];

}

#ifdef __cplusplus

}

#endif

htslib/sam_internal.h at develop · SelfHacked/htslib · GitHub

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