diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/notes.h @ 0:74f5ea818cea

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/notes.h	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,92 @@
+/* 
+ * File:   notes.h
+ * Author: rgoya
+ *
+ * Created on February 3, 2010, 12:37 PM
+ */
+
+/*! @typedef
+@abstract Structure for one alignment covering the pileup position.
+@field  b      pointer to the alignment
+@field  qpos   position of the read base at the pileup site, 0-based
+@field  indel  indel length; 0 for no indel, positive for ins and negative for del
+@field  is_del 1 iff the base on the padded read is a deletion
+@field  level  the level of the read in the "viewer" mode
+
+@discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
+difference between the two functions is that the former does not
+set bam_pileup1_t::level, while the later does. Level helps the
+implementation of alignment viewers, but calculating this has some
+overhead.
+*/
+typedef struct {
+	bam1_t *b;
+	int32_t qpos;
+	int indel, level;
+	uint32_t is_del:1, is_head:1, is_tail:1;
+} bam_pileup1_t;
+
+/*! @typedef
+  @abstract Structure for core alignment information.
+  @field  tid     chromosome ID, defined by bam_header_t
+  @field  pos     0-based leftmost coordinate
+  @field  strand  strand; 0 for forward and 1 otherwise
+  @field  bin     bin calculated by bam_reg2bin()
+  @field  qual    mapping quality
+  @field  l_qname length of the query name
+  @field  flag    bitwise flag
+  @field  n_cigar number of CIGAR operations
+  @field  l_qseq  length of the query sequence (read)
+ */
+typedef struct {
+	int32_t tid;
+	int32_t pos;
+	uint32_t bin:16, qual:8, l_qname:8;
+	uint32_t flag:16, n_cigar:16;
+	int32_t l_qseq;
+	int32_t mtid;
+	int32_t mpos;
+	int32_t isize;
+} bam1_core_t;
+
+/*! @typedef
+  @abstract Structure for one alignment.
+  @field  core       core information about the alignment
+  @field  l_aux      length of auxiliary data
+  @field  data_len   current length of bam1_t::data
+  @field  m_data     maximum length of bam1_t::data
+  @field  data       all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
+
+  @discussion Notes:
+
+   1. qname is zero tailing and core.l_qname includes the tailing '\0'.
+   2. l_qseq is calculated from the total length of an alignment block
+      on reading or from CIGAR.
+ */
+typedef struct {
+	bam1_core_t core;
+	int l_aux, data_len, m_data;
+	uint8_t *data;
+} bam1_t;
+
+
+/*! @typedef
+@abstract Structure for one alignment covering the pileup position.
+@field  b      pointer to the alignment
+@field  qpos   position of the read base at the pileup site, 0-based
+@field  indel  indel length; 0 for no indel, positive for ins and negative for del
+@field  is_del 1 iff the base on the padded read is a deletion
+@field  level  the level of the read in the "viewer" mode
+
+@discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
+difference between the two functions is that the former does not
+set bam_pileup1_t::level, while the later does. Level helps the
+implementation of alignment viewers, but calculating this has some
+overhead.
+*/
+typedef struct {
+	bam1_t *b;
+	int32_t qpos;
+	int indel, level;
+	uint32_t is_del:1, is_head:1, is_tail:1;
+} bam_pileup1_t;