d2c7e8be3ceae6027a5274faafdf6239d778cc63
aamp
  Sat Jul 16 08:31:16 2011 -0700
Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
diff --git src/hg/inc/bamFile.h src/hg/inc/bamFile.h
deleted file mode 100644
index c22350c..0000000
--- src/hg/inc/bamFile.h
+++ /dev/null
@@ -1,52 +0,0 @@
-/* bamFile -- interface to binary alignment format files using Heng Li's samtools lib. */
-
-#ifndef BAMFILE_H
-#define BAMFILE_H
-
-#ifndef BAMUDC_H
-#include "bamUdc.h"
-#endif
-
-#ifdef USE_BAM
-
-#ifndef SAMALIGNMENT_H
-#include "samAlignment.h"
-#endif
-
-#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 */
-
-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 BAMFILE_H