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/inc/bamFile.h src/inc/bamFile.h
index 4c27828..499402c 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -1,98 +1,74 @@
 /* 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
-#ifdef USE_HTS
 #include "htslib/sam.h"
 typedef samFile samfile_t;
 typedef hts_idx_t bam_index_t;
 typedef bam_hdr_t bam_header_t;
 typedef int (*bam_fetch_f)(const bam1_t *bam, void *data, bam_hdr_t *header) ;
 #define samopen(a,b,c) sam_open(a,b)
 #define samclose(a) sam_close(a)
 #define bam1_qname bam_get_qname
 #define bam1_qual bam_get_qual
 #define bam1_aux bam_get_aux
 #define bam1_cigar bam_get_cigar
 #define bam1_seq bam_get_seq
 #define bam1_seqi bam_seqi
 #define bam_nt16_rev_table seq_nt16_str
 #define data_len l_data
-#else
-#include "bam.h"
-#include "sam.h"
-#endif
-
-#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
 
 struct bamChromInfo
     {
     struct bamChromInfo *next;
     char *name;		/* Chromosome name */
     bits32 size;	/* Chromosome size in bases */
     };
 
 boolean bamFileExists(char *bamFileName);
 /* Return TRUE if we can successfully open the bam file and its index file. */
 
 void bamFileAndIndexMustExist(char *fileOrUrl);
 /* Open both a bam file and its accompanying index or errAbort; this is what it
  * takes for diagnostic info to propagate up through errCatches in calling code. */
 
 samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName);
 /* Return an open bam file as well as the filename of the bam. */
 
 samfile_t *bamMustOpenLocal(char *fileName, char *mode, void *extraHeader);
 /* Open up sam or bam file or die trying.  The mode parameter is 
  *    "r" - open SAM to read
  *    "rb" - open BAM to read
  *    "w" - open SAM to write
  *    "wb" - open BAM to write
  * The extraHeader is generally NULL in the read case, and the write case
  * contains a pointer to a bam_header_t with information about the header.
  * The implementation is just a wrapper around samopen from the samtools library
  * that aborts with error message if there's a problem with the open. */
 
-#ifdef USE_HTS
 void bamFetchAlreadyOpen(samfile_t *samfile, bam_hdr_t *header,  bam_index_t *idx, char *bamFileName, 
-#else
-void bamFetchAlreadyOpen(samfile_t *samfile, bam_index_t *idx, char *bamFileName, 
-#endif
 			 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 bamFetchPlus(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
 		 samfile_t **pSamFile, char *refUrl, char *cacheDir);
 /* 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.  
  * refUrl points to the place to grab CRAM reference sequences (if any)
  * cacheDir points to the directory in which CRAM reference sequences are cached */
@@ -104,46 +80,41 @@
  * 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_core(), long may it remain stable:
 #define BAM_DOT_C_OPCODE_STRING "MIDNSHP=X"
 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);