1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
|
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
package ngs;
/**
* Represents a single cell of a sparse 2D matrix with Reference coordinates on one axis
* and stacked Alignments on the other axis
*/
public interface PileupEvent
{
/*----------------------------------------------------------------------
* Reference
*/
/**
* getMappingQuality
* @return the mapping quality
* @throws ErrorMsg upon an error accessing data
*/
int getMappingQuality ()
throws ErrorMsg;
/*----------------------------------------------------------------------
* Alignment
*/
/**
* getAlignmentId
* @return unique AlignmentId within ReadCollection
* @throws ErrorMsg upon an error accessing data
*/
String getAlignmentId ()
throws ErrorMsg;
/**
* getAlignmentPosition
* @return Position of the alignment in Reference coordinates
* @throws ErrorMsg upon an error accessing data
*/
long getAlignmentPosition ()
throws ErrorMsg;
/**
* getFirstAlignmentPosition
* @return the position of this Alignment's first event in Reference coordinates
* @throws ErrorMsg upon an error accessing data
*/
long getFirstAlignmentPosition ()
throws ErrorMsg;
/**
* getLastAlignmentPosition
* @return the position of this Alignment's last event in INCLUSIVE Reference coordinates
* @throws ErrorMsg upon an error accessing data
*/
long getLastAlignmentPosition ()
throws ErrorMsg;
/*----------------------------------------------------------------------
* event details
*/
/**
* EventType
*/
// event types representable in reference coordinate space
static int match = 0;
static int mismatch = 1;
static int deletion = 2;
// an insertion cannot be represented in reference coordinate
// space ( so no insertion event can be directly represented ),
// but it can occur before a match or mismatch event.
// insertion is represented as a bit
static int insertion = 0x08;
// insertions into the reference
static int insertion_before_match = insertion | match;
static int insertion_before_mismatch = insertion | mismatch;
// simultaneous insertion and deletion,
// a.k.a. a replacement
static int insertion_before_deletion = insertion | deletion;
static int replacement = insertion_before_deletion;
// additional modifier bits - may be added to any event above
static int alignment_start = 0x80;
static int alignment_stop = 0x40;
static int alignment_minus_strand = 0x20;
/**
* getEventType
* @return the type of event being represented
* @throws ErrorMsg upon an error accessing data
*/
int getEventType ()
throws ErrorMsg;
/**
* getAlignmentBase
* @return retrieves base aligned at current Reference position
* @throws ErrorMsg if event is an insertion or deletion
*/
char getAlignmentBase ()
throws ErrorMsg;
/**
* getAlignmentQuality
* @return retrieves base aligned at current Reference position
* @throws ErrorMsg if event is an insertion or deletion
*/
char getAlignmentQuality ()
throws ErrorMsg;
/**
* getInsertionBases
* @return bases corresponding to insertion event
* @throws ErrorMsg upon an error accessing data
*/
String getInsertionBases ()
throws ErrorMsg;
/**
* getInsertionQualities
* @return qualities corresponding to insertion event
* @throws ErrorMsg upon an error accessing data
*/
String getInsertionQualities ()
throws ErrorMsg;
/**
* getEventRepeatCount
* @return the number of times this event repeats, i.e. the distance to the first reference position yielding a different event type for this alignment
* @throws ErrorMsg upon an error accessing data
*/
int getEventRepeatCount ()
throws ErrorMsg;
/**
* EventIndelType
*/
static int normal_indel = 0;
// introns behave like deletions
// (i.e. can retrieve deletion count),
// "_plus" and "_minus" signify direction
// of transcription if known
static int intron_plus = 1;
static int intron_minus = 2;
static int intron_unknown = 3;
// overlap is reported as an insertion,
// but is actually an overlap in the read
// inherent in technology like Complete Genomics
static int read_overlap = 4;
// gap is reported as a deletion,
// but is actually a gap in the read
// inherent in technology like Complete Genomics
static int read_gap = 5;
/**
* getEventIndelType
* @return detail about the type of indel when event type is an insertion or deletion
* @throws ErrorMsg upon an error accessing data
*/
int getEventIndelType ()
throws ErrorMsg;
}
|
