9d7ad023de1fe5c42d386f3793fb87b80732d607
angie
  Tue Feb 8 11:48:18 2011 -0800
Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1.
Fix: add stub routines to bamFile.c so that the compile won't break,
but informative error message will be printed if bamFile routines are
called.  I was hoping that this would obviate most of the #ifdef USE_BAM's
currently in the tree, but actually most of those prevent CGIs from
getting into trouble by offering BAM functionality when it isn't
compiled in.  So I left most current #ifdef USE_BAM's in place, but
when future new code doesn't #ifdef, at least the compile won't break.

diff --git src/hg/inc/bamFile.h src/hg/inc/bamFile.h
index 40fc1d1..a7cea23 100644
--- src/hg/inc/bamFile.h
+++ src/hg/inc/bamFile.h
@@ -1,111 +1,132 @@
-/* bamFILE -- interface to binary alignment format files using Heng Li's samtools lib. */
+/* bamFile -- interface to binary alignment format files using Heng Li's samtools lib. */
 
 #ifndef BAMFILE_H
 #define BAMFILE_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 { } 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 SAMALIGNMENT_H
 #include "samAlignment.h"
 #endif
 
 #ifndef DNASEQ_H
 #include "dnaseq.h"
 #endif
 
 #ifndef JKSQL_H
 #include "jksql.h"
 #endif 
 
 char *bamFileNameFromTable(struct sqlConnection *conn, 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 *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.  */
 
 struct samAlignment *bamFetchSamAlignment(char *fileOrUrl, char *chrom, int start, int end,
 	struct lm *lm);
 /* Fetch region as a list of samAlignments - which is more or less an unpacked
  * bam record.  Results is allocated out of lm, since it tends to be large... */
 
 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). */
 
 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. */
 
 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,
 			 boolean useStrand, char **retQSeq);
 /* Convert from bam to ffAli format.  If retQSeq is non-null, set it to the 
  * query sequence into which ffAli needle pointers point. */
 
 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