X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam.h;h=4c8536fd33366883028ff9b77bb95049682c5f9f;hb=c9a9c2742eecde8e097f70efdb6d599374ca325e;hp=fb71a49b46dafea0512a99e157735104cd3832a3;hpb=a958954399757774ee26bfcf0b5b95e9ec9b62f4;p=samtools.git

diff --git a/bam.h b/bam.h
index fb71a49..4c8536f 100644
--- a/bam.h
+++ b/bam.h
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2008-2010 Genome Research Ltd (GRL).
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -230,7 +230,7 @@ typedef struct __bam_iter_t *bam_iter_t;
   @param  b  pointer to an alignment
   @return    pointer to quality string
  */
-#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + ((b)->core.l_qseq + 1)/2)
+#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
 
 /*! @function
   @abstract  Get a base on read
@@ -329,6 +329,7 @@ extern "C" {
 	  be destroyed in the first place.
 	 */
 	int sam_header_parse(bam_header_t *h);
+	int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
 
 	/*!
 	  @abstract       Parse @RG lines a update a header struct
@@ -454,6 +455,21 @@ extern "C" {
 
 	char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
 
+	/*!
+	  @abstract       Check whether a BAM record is plausibly valid
+	  @param  header  associated header structure, or NULL if unavailable
+	  @param  b       alignment to validate
+	  @return         0 if the alignment is invalid; non-zero otherwise
+
+	  @discussion  Simple consistency check of some of the fields of the
+	  alignment record.  If the header is provided, several additional checks
+	  are made.  Not all fields are checked, so a non-zero result is not a
+	  guarantee that the record is valid.  However it is usually good enough
+	  to detect when bam_seek() has been called with a virtual file offset
+	  that is not the offset of an alignment record.
+	 */
+	int bam_validate1(const bam_header_t *header, const bam1_t *b);
+
 	const char *bam_get_library(bam_header_t *header, const bam1_t *b);
 
 
@@ -479,7 +495,7 @@ extern "C" {
 		bam1_t *b;
 		int32_t qpos;
 		int indel, level;
-		uint32_t is_del:1, is_head:1, is_tail:1;
+		uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1;
 	} bam_pileup1_t;
 
 	typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);