src/hg/inc/bamFile.h 1.13

Index: src/hg/inc/bamFile.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/bamFile.h,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 1000000 -r1.12 -r1.13
--- src/hg/inc/bamFile.h	19 Oct 2009 22:50:07 -0000	1.12
+++ src/hg/inc/bamFile.h	10 Dec 2009 15:02:12 -0000	1.13
@@ -1,86 +1,84 @@
 /* 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:
+#ifndef _IOLIB
 #define _IOLIB 2
+#endif
 #include "bam.h"
 #include "sam.h"
 
-void bamIgnoreStrand();
-/* Change the behavior of this lib to disregard item strand. 
- * If called, this should be called before any other bam functions. */
-
 char *bamFileNameFromTable(char *db, char *table, char *bamSeqName);
 /* Return file name from table.  If table has a seqName column, then grab the 
  * row associated with bamSeqName (which is not nec. in chromInfo, e.g. 
  * bam file might have '1' not 'chr1'). */
 
 boolean bamFileExists(char *bamFileName);
 /* Return TRUE if we can successfully open the bam file and its index file. */
 
 void bamFetch(char *bamFileName, char *position, bam_fetch_f callbackFunc, void *callbackData);
 /* 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. 
- * Note: if sequences in .bam file don't begin with "chr" but cart position does, pass in 
- * cart position + strlen("chr") to match the .bam file sequence names. */
+ * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. */
 
 boolean bamIsRc(const bam1_t *bam);
-/* Return TRUE if alignment is on - strand.  If bamIgnoreStrand has been called,
- * then this always returns FALSE. */
+/* 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. */
 {
 // 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);
+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 here we rev-comp it back to restore the original query sequence. */
+ * so if useStrand is given we rev-comp it back to restore the original query 
+ * sequence. */
 
-UBYTE *bamGetQueryQuals(const bam1_t *bam);
+UBYTE *bamGetQueryQuals(const bam1_t *bam, boolean useStrand);
 /* Return the base quality scores encoded in bam as an array of ubytes. */
 
 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. */
 
-struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset);
+struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset,
+			 boolean useStrand);
 /* Convert from bam to ffAli format. */
 
 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. */
 
 #endif//ndef BAMFILE_H