X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam.h;h=cd2455af2337cd2884249ed308cbbeb6873eea1a;hb=4dde8f521add6fbc60641a280e38136c7b9e6ae5;hp=f3f37f3ecefff6509b7480c52eed0f0090a1fd2f;hpb=e04c20c4c76cb19dc015dfa1d733f5473c34134f;p=samtools.git

diff --git a/bam.h b/bam.h
index f3f37f3..cd2455a 100644
--- a/bam.h
+++ b/bam.h
@@ -40,7 +40,11 @@
   @copyright Genome Research Ltd.
  */
 
-#define BAM_VERSION "0.1.18-r572"
+#ifndef VERSION
+#define BAM_VERSION "0.1.19+"
+#else
+#define BAM_VERSION VERSION
+#endif
 
 #include <stdint.h>
 #include <stdlib.h>
@@ -168,7 +172,6 @@ typedef struct {
   @abstract Structure for core alignment information.
   @field  tid     chromosome ID, defined by bam_header_t
   @field  pos     0-based leftmost coordinate
-  @field  strand  strand; 0 for forward and 1 otherwise
   @field  bin     bin calculated by bam_reg2bin()
   @field  qual    mapping quality
   @field  l_qname length of the query name
@@ -193,13 +196,15 @@ typedef struct {
   @field  l_aux      length of auxiliary data
   @field  data_len   current length of bam1_t::data
   @field  m_data     maximum length of bam1_t::data
-  @field  data       all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
+  @field  data       all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
 
   @discussion Notes:
  
    1. qname is zero tailing and core.l_qname includes the tailing '\0'.
    2. l_qseq is calculated from the total length of an alignment block
       on reading or from CIGAR.
+   3. cigar data is encoded 4 bytes per CIGAR operation.
+   4. seq is nybble-encoded according to bam_nt16_table.
  */
 typedef struct {
 	bam1_core_t core;
@@ -772,7 +777,7 @@ static inline int bam_aux_type2size(int x)
 {
 	if (x == 'C' || x == 'c' || x == 'A') return 1;
 	else if (x == 'S' || x == 's') return 2;
-	else if (x == 'I' || x == 'i' || x == 'f') return 4;
+	else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4;
 	else return 0;
 }