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 (<A HREF=\"http://samtools.sourceforge.net\" " \ "TARGET=_BLANK>http://samtools.sourceforge.net</A>) and recompile kent/src with " \ "USE_BAM=1 in your environment " \ "(see <A HREF=\"http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables\" " \ "TARGET=_BLANK>http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables</A>)." #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