f3fd89193f28ab85e5c51c52f20b7c8400c26350
larrym
  Tue Jan 10 15:38:06 2012 -0800
move chrom name normalizing code out of bamFile (we weren't handling stuff like 'IV' and '2L')
diff --git src/inc/bamFile.h src/inc/bamFile.h
index 8ecc78c..4563773 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -1,147 +1,148 @@
 /* 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
 #include "bam.h"
 #include "sam.h"
 
 #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. */
 
 samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName);
 /* Return an open bam file as well as the filename of the bam. */
 
 void bamFetchAlreadyOpen(samfile_t *samfile, 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 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. */
 {
 #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);
 /* 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 */
 
 struct bamChromInfo *bamChromList(samfile_t *fh);
-/* Return list of chromosomes from bam header. We normalize chromosome names to UCSC format. */
+/* 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 */
 
 #endif//ndef BAMFILE_H