/usr/include/bambamc/BamBam_BamFileHeader.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 | /**
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_BAMFILEHEADER_H)
#define BAMBAM_BAMFILEHEADER_H
#include <stdint.h>
#include <bambamc/BamBam_List.h>
#include <bambamc/BamBam_Chromosome.h>
#include <bambamc/BamBam_GzipReader.h>
typedef struct _BamBam_BamFileHeader
{
/* length of orignal text */
int32_t l_text;
/* original text */
char * text;
/* number of chromosomes/references */
int32_t n_ref;
/* linked list of chromosomes */
BamBam_List * chromosomes;
/* chromosomes in numerical id order */
BamBam_Chromosome ** chromosomevec;
/* chromosomes in name sorted order */
BamBam_Chromosome ** sortedchromosomevec;
/* single header lines */
char ** headerlines;
/* HD header line */
char const * hdline;
/* sort order (coordinate or queryname) */
char * sortorder;
/* bam file version */
char * version;
/* processed header text */
char * headertext;
} BamBam_BamFileHeader;
extern BamBam_BamFileHeader * BamBam_BamFileHeader_New_SAM(FILE * reader);
extern BamBam_BamFileHeader * BamBam_BamFileHeader_New_BAM(BamBam_GzipReader * reader);
extern BamBam_BamFileHeader * BamBam_BamFileHeader_Delete(BamBam_BamFileHeader * object);
extern BamBam_Chromosome const * BamBam_BamFileHeader_FindChromosomeByName(BamBam_BamFileHeader const * header, char const * name);
extern int BamBam_BamFileHeader_FindChromosomeIdByName(BamBam_BamFileHeader const * header, char const * name);
#endif
|