X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.h;h=346c750c8c807c44ea32804eeb1bb93411d0b71a;hp=8e26ea69d3b7c6b008aba6112052310a4072b08a;hb=9a36c994ed991f79cc191ece6cbc5f1bf6410da2;hpb=cb12a866906ec4ac644de0e658679261c82ab098

diff --git a/bam.h b/bam.h
index 8e26ea6..346c750 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
@@ -33,13 +33,15 @@
 
   BAM library provides I/O and various operations on manipulating files
   in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
-  format. It now supports importing from or exporting to TAM, sorting,
+  format. It now supports importing from or exporting to SAM, sorting,
   merging, generating pileup, and quickly retrieval of reads overlapped
   with a specified region.
 
   @copyright Genome Research Ltd.
  */
 
+#define BAM_VERSION "0.1.18 (r982:295)"
+
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>
@@ -132,20 +134,25 @@ 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
 
 /*! @typedef
   @abstract Structure for core alignment information.
@@ -230,7 +237,7 @@ 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
@@ -262,6 +269,12 @@ typedef struct __bam_iter_t *bam_iter_t;
  */
 extern int bam_is_be;
 
+/*!
+  @abstract Verbose level between 0 and 3; 0 is supposed to disable all
+  debugging information, though this may not have been implemented.
+ */
+extern int bam_verbose;
+
 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
 extern unsigned char bam_nt16_table[256];
 
@@ -455,6 +468,21 @@ 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 +508,7 @@ 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, aux:28;
 	} bam_pileup1_t;
 
 	typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
@@ -493,6 +521,7 @@ extern "C" {
 	const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
 	const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
 	void bam_plp_set_mask(bam_plp_t iter, int mask);
+	void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
 	void bam_plp_reset(bam_plp_t iter);
 	void bam_plp_destroy(bam_plp_t iter);
 
@@ -501,6 +530,7 @@ extern "C" {
 
 	bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
 	void bam_mplp_destroy(bam_mplp_t iter);
+	void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
 	int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
 
 	/*! @typedef
@@ -693,8 +723,8 @@ static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
 {
 	uint8_t *data = bdst->data;
 	int m_data = bdst->m_data;   // backup data and m_data
-	if (m_data < bsrc->m_data) { // double the capacity
-		m_data = bsrc->m_data; kroundup32(m_data);
+	if (m_data < bsrc->data_len) { // double the capacity
+		m_data = bsrc->data_len; kroundup32(m_data);
 		data = (uint8_t*)realloc(data, m_data);
 	}
 	memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
@@ -721,4 +751,13 @@ static inline bam1_t *bam_dup1(const bam1_t *src)
 	return b;
 }
 
+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 return 0;
+}
+
+
 #endif