src/hg/inc/bamFile.h 1.6
1.6 2009/08/21 22:52:35 angie
Added bamClone. Fixed bamToFfAli to walk through CIGAR operations backwards when strand is -.
Index: src/hg/inc/bamFile.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/bamFile.h,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/inc/bamFile.h 21 Aug 2009 05:22:01 -0000 1.5
+++ src/hg/inc/bamFile.h 21 Aug 2009 22:52:35 -0000 1.6
@@ -1,50 +1,53 @@
/* bamFILE -- interface to binary alignment format files using Heng Li's samtools lib. */
#ifndef BAMFILE_H
#define BAMFILE_H
// bam.h is incomplete without _IOLIB set to 1, 2 or 3. 2 is used by Makefile.generic:
#define _IOLIB 2
#include "bam.h"
#include "sam.h"
void bamFetch(char *db, char *table, char *position, bam_fetch_f callbackFunc, void *callbackData);
/* Open the .bam file given in db.table, fetch items in the seq:start-end position range,
* and call callbackFunc on each bam item retrieved from the file plus callbackData.
* Note: if sequences in .bam file don't begin with "chr" but db's do, skip the "chr"
* at the beginning of the position. */
INLINE int bamUnpackCigarElement(unsigned int packed, char *retOp)
/* Given an unsigned int containing a number of bases and an offset into an
* array of BAM-enhanced-CIGAR ASCII characters (operations), store operation
* char into *retOp (retOp must not be NULL) and return the number of bases. */
{
// decoding lifted from samtools bam.c bam_format1(), long may it remain stable:
#define BAM_DOT_C_OPCODE_STRING "MIDNSHP"
int n = packed>>BAM_CIGAR_SHIFT;
int opcode = packed & BAM_CIGAR_MASK;
if (opcode >= strlen(BAM_DOT_C_OPCODE_STRING))
errAbort("bamUnpackCigarElement: unrecognized opcode %d. "
"(I only recognize 0..%lu [" BAM_DOT_C_OPCODE_STRING "]) "
"Perhaps samtools bam.c's bam_format1 encoding changed? If so, update me.",
opcode, (unsigned long)(strlen(BAM_DOT_C_OPCODE_STRING)-1));
*retOp = BAM_DOT_C_OPCODE_STRING[opcode];
return n;
}
char *bamGetQuerySequence(const bam1_t *bam);
/* Return the nucleotide sequence encoded in bam. The BAM format
* reverse-complements query sequence when the alignment is on the - strand,
* so here we rev-comp it back to restore the original query sequence. */
char *bamGetCigar(const bam1_t *bam);
/* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */
int bamGetTargetLength(const bam1_t *bam);
/* Tally up the alignment's length on the reference sequence from
* bam's packed-int CIGAR representation. */
struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset);
/* Convert from bam to ffAli format. */
+bam1_t *bamClone(const bam1_t *bam);
+/* Return a newly allocated copy of bam. */
+
#endif//ndef BAMFILE_H