/usr/include/bambamc/BamBam_BamCollator.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 | /**
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_BAMCOLLATOR_H)
#define BAMBAM_BAMCOLLATOR_H
#include <bambamc/BamBam_Unused.h>
#include <bambamc/BamBam_BamCollationHash.h>
#include <bambamc/BamBam_BamCollationVector.h>
#include <bambamc/BamBam_BamCollationOutputVector.h>
#include <bambamc/BamBam_MergeHeapEntry.h>
#include <bambamc/BamBam_BamHeaderInfo.h>
#include <bambamc/BamBam_SamBamFileDecoder.h>
#include <bambamc/BamBam_GzipFileDecoder.h>
#include <bambamc/BamBam_Config.h>
typedef struct _BamBam_BamCollator
{
int state;
int tmpdirstate;
char * tempdirname;
char * tempprefix;
BamBam_BamCollationHash * hash;
BamBam_BamCollationVector * vector;
BamBam_BamCollationTempFileGenerator * gen;
BamBam_BamCollationOutputVector * outputvector;
BamBam_SamBamFileDecoder * decoder;
/* header text */
char * bamheadertext;
char * filteredbamheadertext;
char * headerline;
char * vn;
char * so;
BamBam_BamHeaderInfo * parsedheaderinfo;
BamBam_BamHeaderInfo * headerinfo;
BamBam_BamSingleAlignment * alignment;
uint64_t nummergefiles;
BamBam_GzipFileDecoder ** mergefiles;
BamBam_MergeHeapEntry * mergeheap;
uint64_t mergeheapfill;
char * bufferA;
unsigned int bufferALength;
char * bufferB;
unsigned int bufferBLength;
int keepOrphans;
BamBam_BamCollationHashEntry * entryA;
BamBam_BamCollationHashEntry * entryB;
} BamBam_BamCollator;
extern void BamBam_BamCollator_MergeHeapEntrySwap(BamBam_MergeHeapEntry * A, BamBam_MergeHeapEntry * B);
extern void BamBam_BamCollator_MergeHeapPrint(BamBam_BamCollator * collator);
extern void BamBam_BamCollator_MergeHeapCheck(BamBam_BamCollator * collator);
extern BamBam_MergeHeapEntry * BamBam_BamCollator_MergeHeapMinimum(BamBam_BamCollator * collator) BAMBAM_WARN_IF_UNUSEDRESULT;
extern void BamBam_BamCollator_MergeHeapDeleteMinimum(BamBam_BamCollator * collator);
extern void BamBam_BamCollator_MergeHeapInsert(BamBam_BamCollator * collator, BamBam_BamCollationHashEntry * hashentry, unsigned int fileid);
extern BamBam_BamCollationHashEntry * BamBam_BamCollator_GetNextRead(BamBam_BamCollator * collator) BAMBAM_WARN_IF_UNUSEDRESULT;
extern BamBam_BamCollator * BamBam_BamCollator_Delete(BamBam_BamCollator * collator);
extern BamBam_BamCollator * BamBam_BamCollator_New(
char const * tempdirname,
unsigned int const hashsizelog,
unsigned int const vectorsizelog,
char const * inputformat,
char const * inputfilename
) BAMBAM_WARN_IF_UNUSEDRESULT;
extern int BamBam_BamCollator_Get(
BamBam_BamCollator * collator,
BamBam_BamCollationHashEntry ** entryA,
BamBam_BamCollationHashEntry ** entryB) BAMBAM_WARN_IF_UNUSEDRESULT;
#endif
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