/usr/include/bambamc/BamBam_BamSingleAlignment.h is in libbambamc-dev 0.0.50-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 | /**
bambamc
Copyright (C) 2009-2013 German Tischler
Copyright (C) 2011-2013 Genome Research Limited
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
**/
#if ! defined(BAMBAM_BAMSINGLEALIGNMENT_H)
#define BAMBAM_BAMSINGLEALIGNMENT_H
#include <bambamc/BamBam_BamFileHeader.h>
#include <bambamc/BamBam_CharBuffer.h>
#include <bambamc/BamBam_GzipWriter.h>
#include <bambamc/BamBam_BgzfCompressor.h>
#include <string.h>
typedef enum _bambamc_alignment_validity {
bambamc_alignment_validity_ok = 0,
bambamc_alignment_validity_block_too_small = 1,
bambamc_alignment_validity_queryname_extends_over_block = 2,
bambamc_alignment_validity_queryname_length_inconsistent = 3,
bambamc_alignment_validity_cigar_extends_over_block = 4,
bambamc_alignment_validity_sequence_extends_over_block = 5,
bambamc_alignment_validity_quality_extends_over_block = 6,
bambamc_alignment_validity_cigar_is_inconsistent_with_sequence_length = 7,
bambamc_alignment_validity_unknown_cigar_op = 8,
bambamc_alignment_validity_queryname_contains_illegal_symbols = 9,
bambamc_alignment_validity_queryname_empty = 10,
bambamc_alignment_validity_invalid_mapping_position = 11,
bambamc_alignment_validity_invalid_next_mapping_position = 12,
bambamc_alignment_validity_invalid_tlen = 13,
bambamc_alignment_validity_invalid_quality_value = 14,
bambamc_alignment_validity_invalid_refseq = 15,
bambamc_alignment_validity_invalid_next_refseq = 16,
bambamc_alignment_validity_invalid_auxiliary_data = 17,
bambamc_alignment_valididy_record_length_negative = 18
} bambamc_alignment_validity;
typedef struct _BamBam_BamSingleAlignment
{
uint8_t * data;
uint32_t dataav;
uint32_t dataused;
char * query;
int32_t queryspace;
char * qual;
int32_t qualspace;
char * cigar;
int32_t cigarspace;
bambamc_alignment_validity valid;
BamBam_CharBuffer * auxbuffer;
}
BamBam_BamSingleAlignment;
extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_Delete(BamBam_BamSingleAlignment * data);
extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_New();
extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_NewClone(uint8_t const * block, uint32_t const blocksize);
extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_Clone(BamBam_BamSingleAlignment const * o);
extern int BamBam_BamSingleAlignment_LoadAlignment(BamBam_BamSingleAlignment * data, BamBam_GzipReader * reader);
extern int BamBam_BamSingleAlignment_StoreAlignment(BamBam_BamSingleAlignment const * data, BamBam_GzipWriter * writer);
extern int BamBam_BamSingleAlignment_StoreAlignmentBgzf(BamBam_BamSingleAlignment const * data, BamBam_BgzfCompressor * writer);
extern int32_t BamBam_BamSingleAlignment_GetRefId(BamBam_BamSingleAlignment const * data);
extern int32_t BamBam_BamSingleAlignment_GetPos(BamBam_BamSingleAlignment const * data);
extern uint32_t BamBam_BamSingleAlignment_GetBinMQNL(BamBam_BamSingleAlignment const * data);
extern uint32_t BamBam_BamSingleAlignment_GetBin(BamBam_BamSingleAlignment const * data);
extern uint32_t BamBam_BamSingleAlignment_GetMQ(BamBam_BamSingleAlignment const * data);
extern uint32_t BamBam_BamSingleAlignment_GetNL(BamBam_BamSingleAlignment const * data);
extern uint32_t BamBam_BamSingleAlignment_GetFlagNC(BamBam_BamSingleAlignment const * data);
extern uint32_t BamBam_BamSingleAlignment_GetFlags(BamBam_BamSingleAlignment const * data);
extern uint32_t BamBam_BamSingleAlignment_GetNC(BamBam_BamSingleAlignment const * data);
extern int32_t BamBam_BamSingleAlignment_GetLSeq(BamBam_BamSingleAlignment const * data);
extern int32_t BamBam_BamSingleAlignment_GetNextRefID(BamBam_BamSingleAlignment const * data);
extern int32_t BamBam_BamSingleAlignment_GetNextPos(BamBam_BamSingleAlignment const * data);
extern int32_t BamBam_BamSingleAlignment_GetTLen(BamBam_BamSingleAlignment const * data);
extern char const * BamBam_BamSingleAlignment_GetReadName(BamBam_BamSingleAlignment const * data);
extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedCigar(BamBam_BamSingleAlignment const * data);
extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedQuery(BamBam_BamSingleAlignment const * data);
extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedQual(BamBam_BamSingleAlignment const * data);
extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedAux(BamBam_BamSingleAlignment const * data);
extern int BamBam_BamSingleAlignment_DecodeQueryRc(BamBam_BamSingleAlignment * algn, int const rc);
extern int BamBam_BamSingleAlignment_DecodeQualRc(BamBam_BamSingleAlignment * algn, int const rc);
extern int BamBam_BamSingleAlignment_DecodeCigarRc(BamBam_BamSingleAlignment * algn, int const rc);
extern int BamBam_BamSingleAlignment_DecodeQuery(BamBam_BamSingleAlignment * algn);
extern int BamBam_BamSingleAlignment_DecodeQual(BamBam_BamSingleAlignment * algn);
extern int BamBam_BamSingleAlignment_DecodeCigar(BamBam_BamSingleAlignment * algn);
extern int32_t BamBam_BamSingleAlignment_DecodeQueryQualCigarRc(
BamBam_BamSingleAlignment * algn, int32_t rc, int32_t * querylen, int32_t * cigarlen);
extern int32_t BamBam_BamSingleAlignment_DecodeQueryQualCigar(
BamBam_BamSingleAlignment * algn, int32_t * querylen, int32_t * cigarlen);
extern int BamBam_BamSingleAlignment_DecodeAuxSingle(BamBam_BamSingleAlignment * algn,
uint8_t const * p, int reset);
extern char const * BamBam_BamSingleAlignment_DecodeAux(BamBam_BamSingleAlignment * algn);
extern uint8_t const * BamBam_BamSingleAlignment_FindAux(BamBam_BamSingleAlignment const * algn, char const tag[2]);
extern uint64_t BamBam_BamSingleAlignment_GetAuxLength(BamBam_BamSingleAlignment const * algn);
extern char const * BamBam_Alignment_Validity_Str(bambamc_alignment_validity const code);
#endif
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