29356d0b9520b11bb46d22f5c70b8b1a275b5116
kent
  Tue Dec 27 12:06:35 2016 -0800
Removing bamChromInfo structure and the routines to free it.  The routine that made it got deleted a while back for some reason, so I'm just tidying up.

diff --git src/inc/bamFile.h src/inc/bamFile.h
index 91883ba..d11dc14 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -16,37 +16,30 @@
 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
 
 
-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, 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
@@ -155,33 +148,26 @@
 
 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 */
 
-struct bamChromInfo *bamChromList(samfile_t *fh);
-/* Return list of chromosomes from bam header. We make no attempty to normalize chromosome names to UCSC format,
-   so list may contain things like "1" for "chr1", "I" for "chrI", "MT" for "chrM" etc. */
-
-void bamChromInfoFreeList(struct bamChromInfo **pList);
-/* Free a list of dynamically allocated bamChromInfo's */
-
 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