* vcfutils.pl: fixed a typo in help message

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index fb71a49b46dafea0512a99e157735104cd3832a3..a8769e26a38c3dc62ee4ded2dc793a90884d19a3 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
@@ -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);