# Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 8e26ea69d3b7c6b008aba6112052310a4072b08a..4c8536fd33366883028ff9b77bb95049682c5f9f 100644 (file)
--- 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
@@ -455,6 +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);
 
 
@@ -480,7 +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);