26c2f650359cc1c74fb31d96109bc0f8dedbc3d7
angie
  Thu May 30 10:32:19 2019 -0700
Adding BAM and VCF item counts to hubApi's list/tracks function.  Note: older index files may not contain counts.  refs #18869, #23521

diff --git src/inc/bamFile.h src/inc/bamFile.h
index d11dc14..5da2dd1 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -1,173 +1,180 @@
 /* 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"
 
 
 // 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 "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
 
 
 boolean bamFileExists(char *bamFileName);
 /* Return TRUE if we can successfully open the bam file and its index file. */
 
 void bamFileAndIndexMustExist(char *fileOrUrl, char *baiFileOrUrl);
 /* 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. 
  * The parameter baiFileOrUrl can be NULL, defaults of <fileOrUrl>.bai. */
 
 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. */
 
+long long bamFileItemCount(char *fileOrUrl, char *baiFileOrUrl);
+/* Return the total number of mapped items across all sequences in fileOrUrl, using index file.
+ * If baiFileOrUrl is NULL, the index file is assumed to be fileOrUrl.bai.
+ * NOTE: not all bam index files include mapped item counts, so this may return 0 even for large
+ * bam.  As of May 2019, our copy of hts_idx_get_stat does not support cram indexes
+ * (perhaps they never include counts?), so this always returns 0 for cram. */
+
 void bamFetchAlreadyOpen(samfile_t *samfile, bam_hdr_t *header,  bam_index_t *idx, char *bamFileName, 
 			 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 bamAndIndexFetchPlus(char *fileOrUrl, char *baiFileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
 		 samfile_t **pSamFile, char *refUrl, char *cacheDir);
 /* Open the .bam file with the .bai index specified by baiFileOrUrl.
  * baiFileOrUrl can be NULL and defaults to <fileOrUrl>.bai.
  * 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.  */
 
 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 */
 
 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.  */
 
 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. */
 {
 // 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;
 }
 
 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);
 /* 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. */
 
 void bamUnpackCigar(const bam1_t *bam, struct dyString *dyCigar);
 /* Unpack CIGAR string into dynamic string */
 
 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. */
 
 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. */
 
 void bamUnpackAux(const bam1_t *bam, struct dyString *dy);
 /* Unpack the tag:type:val part of bam into dy */
 
 void samToBed(char *samIn, char *bedOut);
 /* samToBed - Convert SAM file to a pretty simple minded bed file.. */
 
 void samToOpenBed(char *samIn, FILE *f);
 /* Like samToOpenBed, but the output is the already open file f. */
 
 struct psl *bamToPslUnscored(const bam1_t *bam, const bam_hdr_t *hdr);
 /* Translate BAM's numeric CIGAR encoding into PSL sufficient for cds.c (just coords,
  * no scoring info) */
 
 #endif//ndef BAMFILE_H