f4ab269ea813af98072a989a40558e5d7425512a
angie
Mon Aug 22 10:48:02 2011 -0700
Fix for compiling without USE_BAM: bamFile.h needs to define bam_index_t.
diff --git src/inc/bamFile.h src/inc/bamFile.h
index 911d72c..2c876c7 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -1,138 +1,135 @@
/* bamFile -- interface to binary alignment format files using Heng Li's samtools lib. */
#ifndef BAMFILE_H
#define BAMFILE_H
+#include "dnaseq.h"
+#include "dystring.h"
+
#ifdef USE_BAM
// bam.h is incomplete without _IOLIB set to 1, 2 or 3. 2 is used by Makefile.generic:
#ifndef _IOLIB
#define _IOLIB 2
#endif
#include "bam.h"
#include "sam.h"
#else // no USE_BAM
typedef struct { } bam1_t;
+typedef struct { } bam_index_t;
typedef struct { } samfile_t;
typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
#define COMPILE_WITH_SAMTOOLS "%s: in order to use this functionality you must " \
"install the samtools library (http://samtools.sourceforge.net) and recompile kent/src with " \
"USE_BAM=1 in your environment " \
"(see http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables)."
#endif // USE_BAM
-#ifndef DNASEQ_H
-#include "dnaseq.h"
-#endif
-
-#ifndef DYSTRING_H
-#include "dystring.h"
-#endif
boolean bamFileExists(char *bamFileName);
/* Return TRUE if we can successfully open the bam file and its index file. */
samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName);
/* Return an open bam file as well as the filename of the bam. */
void bamFetchAlreadyOpen(samfile_t *samfile, bam_index_t *idx, char *bamFileName,
char *position, bam_fetch_f callbackFunc, void *callbackData);
/* With the open bam file, return items the same way with the callbacks as with bamFetch() */
/* except in this case use an already-open bam file and index (use bam_index_load and free() for */
/* the index). It seems a little strange to pass the filename in with the open bam, but */
/* it's just used to report errors. */
void bamFetch(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
samfile_t **pSamFile);
/* Open the .bam file, fetch items in the seq:start-end position range,
* and call callbackFunc on each bam item retrieved from the file plus callbackData.
* This handles BAM files with "chr"-less sequence names, e.g. from Ensembl.
* The pSamFile parameter is optional. If non-NULL it will be filled in, just for
* the benefit of the callback function, with the open samFile. */
void bamClose(samfile_t **pSamFile);
/* Close down a samefile_t */
boolean bamIsRc(const bam1_t *bam);
/* Return TRUE if alignment is on - strand. */
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. */
{
#ifdef USE_BAM
// 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;
#else // no USE_BAM
errAbort(COMPILE_WITH_SAMTOOLS, "bamUnpackCigarElement");
return 0;
#endif// USE_BAM
}
void bamGetSoftClipping(const bam1_t *bam, int *retLow, int *retHigh, int *retClippedQLen);
/* If retLow is non-NULL, set it to the number of "soft-clipped" (skipped) bases at
* the beginning of the query sequence and quality; likewise for retHigh at end.
* For convenience, retClippedQLen is the original query length minus soft clipping
* (and the length of the query sequence that will be returned). */
void bamUnpackQuerySequence(const bam1_t *bam, boolean useStrand, char *qSeq);
/* Fill in qSeq with the nucleotide sequence encoded in bam. The BAM format
* reverse-complements query sequence when the alignment is on the - strand,
* so if useStrand is given we rev-comp it back to restore the original query
* sequence. */
char *bamGetQuerySequence(const bam1_t *bam, boolean useStrand);
/* Return the nucleotide sequence encoded in bam. The BAM format
* reverse-complements query sequence when the alignment is on the - strand,
* so if useStrand is given we rev-comp it back to restore the original query
* sequence. */
UBYTE *bamGetQueryQuals(const bam1_t *bam, boolean useStrand);
/* Return the base quality scores encoded in bam as an array of ubytes. */
void bamUnpackCigar(const bam1_t *bam, struct dyString *dyCigar);
/* Unpack CIGAR string into dynamic string */
char *bamGetCigar(const bam1_t *bam);
/* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */
void bamShowCigarEnglish(const bam1_t *bam);
/* Print out cigar in English e.g. "20 (mis)Match, 1 Deletion, 3 (mis)Match" */
void bamShowFlagsEnglish(const bam1_t *bam);
/* Print out flags in English, e.g. "Mate is on '-' strand; Properly paired". */
int bamGetTargetLength(const bam1_t *bam);
/* Tally up the alignment's length on the reference sequence from
* bam's packed-int CIGAR representation. */
bam1_t *bamClone(const bam1_t *bam);
/* Return a newly allocated copy of bam. */
void bamShowTags(const bam1_t *bam);
/* Print out tags in HTML: bold key, no type indicator for brevity. */
char *bamGetTagString(const bam1_t *bam, char *tag, char *buf, size_t bufSize);
/* If bam's tags include the given 2-character tag, place the value into
* buf (zero-terminated, trunc'd if nec) and return a pointer to buf,
* or NULL if tag is not present. */
void bamUnpackAux(const bam1_t *bam, struct dyString *dy);
/* Unpack the tag:type:val part of bam into dy */
#endif//ndef BAMFILE_H