173bacbf6c28737266ef93048446902620b49330
braney
  Mon Dec 14 12:33:16 2015 -0800
some tweaks to CRAM support #14717

diff --git src/hg/inc/hgBam.h src/hg/inc/hgBam.h
index 3e0196d..d907ba8 100644
--- src/hg/inc/hgBam.h
+++ src/hg/inc/hgBam.h
@@ -1,45 +1,50 @@
 /* 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... */
 
 #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. */
 
+void cramInit(struct trackDb *tdb);
+/* Initialize variables needed for CRAM parsing. */
+
 #endif//ndef HGBAM_H