af568c29d9e2d2ad91cea882a92c0a8991f7748c
aamp
  Fri Jul 8 16:11:15 2011 +0200
Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it).  Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting.  It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
diff --git src/hg/inc/bamFile.h src/hg/inc/bamFile.h
index b9e2331..c22350c 100644
--- src/hg/inc/bamFile.h
+++ src/hg/inc/bamFile.h
@@ -1,143 +1,52 @@
 /* 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
+#ifndef BAMUDC_H
+#include "bamUdc.h"
 #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
+#ifdef 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 can be e.g. '1' not 'chr1' if that is the
  * case in the bam file). */
 
 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... */
 
 struct samAlignment *bamReadNextSamAlignments(samfile_t *fh, int count, struct lm *lm);
 /* Read next count alignments in SAM format, allocated in lm.  May return less than
  * count at end of file. */
 
 samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName);
 /* Return an open bam file, dealing with FUSE caching if need be. 
  * Return parameter if NON-null will return the file name after FUSing */
 
-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). */
-
-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