X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam.h;h=752d0bda7dea595c3c9014968fee9cd02057662b;hb=fe25084a4eac12a94042805e6529ad19a2b70c28;hp=b418dcd796a171bcdecd71381db6dded02b5ab3a;hpb=a9699b025d1a4b46dd82d2ca77c5c798cc2bd7e3;p=samtools.git

diff --git a/bam.h b/bam.h
index b418dcd..752d0bd 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
@@ -40,6 +40,8 @@
   @copyright Genome Research Ltd.
  */
 
+#define BAM_VERSION "0.1.12-r921:124"
+
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>
@@ -190,7 +192,7 @@ typedef struct {
 	uint8_t *data;
 } bam1_t;
 
-typedef struct __bam_iterf_t *bam_iterf_t;
+typedef struct __bam_iter_t *bam_iter_t;
 
 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
 #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
@@ -230,7 +232,7 @@ typedef struct __bam_iterf_t *bam_iterf_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 +331,7 @@ 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 +457,21 @@ 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);
 
 
@@ -479,10 +497,10 @@ 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)(bam1_t *b, void *data);
+	typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
 
 	struct __bam_plp_t;
 	typedef struct __bam_plp_t *bam_plp_t;
@@ -492,6 +510,7 @@ 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);
 
@@ -500,6 +519,7 @@ 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
@@ -594,9 +614,9 @@ extern "C" {
 	 */
 	int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
 
-	bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end);
-	int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b);
-	void bam_iterf_destroy(bam_iterf_t iter);
+	bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end);
+	int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b);
+	void bam_iter_destroy(bam_iter_t iter);
 
 	/*!
 	  @abstract       Parse a region in the format: "chr2:100,000-200,000".
@@ -692,8 +712,8 @@ 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