11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/hg/inc/hgBam.h src/hg/inc/hgBam.h
index ec530e1..341dc9e 100644
--- src/hg/inc/hgBam.h
+++ src/hg/inc/hgBam.h
@@ -1,52 +1,48 @@
 /* hgBam -- interface to binary alignment format files using Heng Li's samtools lib. */
 /* these are the components that link to MySQL */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #ifndef HGBAM_H
 #define HGBAM_H
 
 #ifndef BAMFILE_H
 #include "bamFile.h"
 #endif
 
 #ifndef SAMALIGNMENT_H
 #include "samAlignment.h"
 #endif
 
 #ifndef JKSQL_H
 #include "jksql.h"
 #endif
 
 #include "trackDb.h"
 
 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). */
 
 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 *bamFetchSamAlignmentPlus(char *fileOrUrl, char *chrom, int start, int end,
 	struct lm *lm, char *refUrl, char *cacheDir );
 /* 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... */
 
-#ifdef USE_HTS
 struct samAlignment *bamReadNextSamAlignments(samfile_t *fh, bam_hdr_t *header,  int count, struct lm *lm);
-#else
-struct samAlignment *bamReadNextSamAlignments(samfile_t *fh, int count, struct lm *lm);
-#endif
 /* Read next count alignments in SAM format, allocated in lm.  May return less than
  * count at end of file. */
 
 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. */
 
 #endif//ndef HGBAM_H