X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam.h;h=11f8028cf6d96ece1390074c6fb155437ce5f766;hb=2594fb7e8055fefc08b37a14ad437aa9bafbe837;hp=246b020d679a07f073cfbae8dc40a8d57b501d25;hpb=3384f6c6c1642ada4edae9204ca1202672de7d5a;p=samtools.git

diff --git a/bam.h b/bam.h
index 246b020..11f8028 100644
--- a/bam.h
+++ b/bam.h
@@ -40,7 +40,7 @@
   @copyright Genome Research Ltd.
  */
 
-#define BAM_VERSION "0.1.17 (r973:277)"
+#define BAM_VERSION "0.1.18-dev (r982:313)"
 
 #include <stdint.h>
 #include <stdlib.h>
@@ -89,7 +89,7 @@ typedef struct {
 	char **target_name;
 	uint32_t *target_len;
 	void *dict, *hash, *rg2lib;
-	size_t l_text, n_text;
+	uint32_t l_text, n_text;
 	char *text;
 } bam_header_t;
 
@@ -134,20 +134,35 @@ typedef struct {
 /*
   CIGAR operations.
  */
-/*! @abstract CIGAR: match */
+/*! @abstract CIGAR: M = match or mismatch*/
 #define BAM_CMATCH      0
-/*! @abstract CIGAR: insertion to the reference */
+/*! @abstract CIGAR: I = insertion to the reference */
 #define BAM_CINS        1
-/*! @abstract CIGAR: deletion from the reference */
+/*! @abstract CIGAR: D = deletion from the reference */
 #define BAM_CDEL        2
-/*! @abstract CIGAR: skip on the reference (e.g. spliced alignment) */
+/*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */
 #define BAM_CREF_SKIP   3
-/*! @abstract CIGAR: clip on the read with clipped sequence present in qseq */
+/*! @abstract CIGAR: S = clip on the read with clipped sequence
+  present in qseq */
 #define BAM_CSOFT_CLIP  4
-/*! @abstract CIGAR: clip on the read with clipped sequence trimmed off */
+/*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */
 #define BAM_CHARD_CLIP  5
-/*! @abstract CIGAR: padding */
+/*! @abstract CIGAR: P = padding */
 #define BAM_CPAD        6
+/*! @abstract CIGAR: equals = match */
+#define BAM_CEQUAL      7
+/*! @abstract CIGAR: X = mismatch */
+#define BAM_CDIFF       8
+#define BAM_CBACK       9
+
+#define BAM_CIGAR_STR  "MIDNSHP=XB"
+#define BAM_CIGAR_TYPE 0x3C1A7
+
+#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
+#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
+#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
+#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
+#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference
 
 /*! @typedef
   @abstract Structure for core alignment information.
@@ -240,7 +255,10 @@ typedef struct __bam_iter_t *bam_iter_t;
   @param  i  The i-th position, 0-based
   @return    4-bit integer representing the base.
  */
-#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+//#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+#define bam1_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)
+
+#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )
 
 /*! @function
   @abstract  Get query sequence and quality
@@ -270,6 +288,8 @@ extern int bam_is_be;
  */
 extern int bam_verbose;
 
+extern int bam_no_B;
+
 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
 extern unsigned char bam_nt16_table[256];
 
@@ -415,6 +435,8 @@ extern "C" {
 	 */
 	int bam_read1(bamFile fp, bam1_t *b);
 
+	int bam_remove_B(bam1_t *b);
+
 	/*!
 	  @abstract Write an alignment to BAM.
 	  @param  fp       BAM file handler