libStatGen Software 1
SamHeaderRecord.cpp
1/*
2 * Copyright (C) 2010 Regents of the University of Michigan
3 *
4 * This program is free software: you can redistribute it and/or modify
5 * it under the terms of the GNU General Public License as published by
6 * the Free Software Foundation, either version 3 of the License, or
7 * (at your option) any later version.
8 *
9 * This program is distributed in the hope that it will be useful,
10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 * GNU General Public License for more details.
13 *
14 * You should have received a copy of the GNU General Public License
15 * along with this program. If not, see <http://www.gnu.org/licenses/>.
16 */
17
18#include "SamHeaderRecord.h"
19
20// Constructor
22 : myTagHash(),
23 myTags(),
24 myNumActiveTags(0)
25{
26}
27
28
29// Destructor
31{
32 reset();
33}
34
35
36// Set the fields from the passed in line.
37// Return true if successfully set.
39{
40 bool status = true;
41
42 // Loop through the tags for this type.
43 // The tags start in column 1 since column 0 contains the type.
44 for(int columnIndex = 1; columnIndex < tokens.Length(); columnIndex++)
45 {
46 // Validate that the tag is at least 3 characters. Two for the token,
47 // one for the ':'.
48 if((tokens[columnIndex].Length() < 3) ||
49 (tokens[columnIndex][2] != ':'))
50 {
51 // Continue to the next tag, this one is too small/invalid.
52 status = false;
53 std::cerr << "ERROR: Poorly formatted tag in header: "
54 << tokens[columnIndex] << std::endl;
55 continue;
56 }
57
58 // Get the tag from the token.
59 char tag[3];
60 tag[0] = tokens[columnIndex][0];
61 tag[1] = tokens[columnIndex][1];
62 tag[2] = 0;
63
64 // The tag value is the rest of the substring.
65 String tagValue = (tokens[columnIndex]).SubStr(3);
66
67 // Set the tag.
68 status &= setTag(tag, tagValue.c_str());
69 }
70
71 status &= isValid();
72
73 return(status);
74}
75
76
77// Check to see if the record is valid.
79{
80 bool status = true;
81 // Check that the required tags are set. If they aren't, return false.
82 for(unsigned int reqIndex = 0; reqIndex < myRequiredTags.size(); reqIndex++)
83 {
84 // Check to see if the required tag at this index exists and has
85 // a value.
86 int index = myTagHash.Integer(myRequiredTags[reqIndex].c_str());
87 if((index < 0) || !(myTags[index]->hasValue()))
88 {
89 // Did not find the tag, stet status to false.
90 std::cerr << "ERROR: Missing required tag: "
91 << myRequiredTags[reqIndex] << "." << std::endl;
92 status = false;
93 }
94 }
95 return(status);
96}
97
98
99// Return the value associated with the specified tag.
100const char* SamHeaderRecord::getTagValue(const char* tag) const
101{
102 // Look up the tag in myTags.
103 int index = myTagHash.Integer(tag);
104 if(index < 0)
105 {
106 // The tag was not found in the hash, so return "".
107 return("");
108 }
109
110 // The tag was found in the hash, so return the tag value found at the
111 // index associated with the tag.
112 return(myTags[index]->getValue());
113}
114
115
116// Set the value of the specified tag to the specified value.
117// Set value to NULL in order to delete the tag.
118// Returns whether or not it was successful.
119bool SamHeaderRecord::setTag(const char* tag, const char* value)
120{
121 // Lookup the tag in the hash.
122 int vectorIndex = myTagHash.Integer(tag);
123 if(vectorIndex < 0)
124 {
125 // The tag was not found in the hash, so create a new one.
126 SamHeaderTag* tagPtr = new SamHeaderTag(tag, value);
127
128 if(tagPtr == NULL)
129 {
130 // Failed to allocate the tag, return false.
131 std::cerr << "Failed to allocate space (new) for a SamHeaderTag.\n";
132 return(false);
133 }
134
135 // Add the new tag to the back of the tag values.
136 vectorIndex = myTags.size();
137 myTags.push_back(tagPtr);
138
139 // If the value is not null, increment the number of active tags.
140 if(value[0] != 0)
141 {
142 ++myNumActiveTags;
143 }
144
145 // Add the tag to the hash.
146 int hashIndex = myTagHash.Add(tag, vectorIndex);
147
148 if((myTagHash.Integer(hashIndex) != vectorIndex) ||
149 (myTagHash[hashIndex] != tag))
150 {
151 // Failed to add the tag, so return false.
152 std::cerr << "Failed to add tag, " << tag
153 << ", to the hash." << std::endl;
154 return(false);
155 }
156 return(true);
157 }
158 else if((unsigned int)vectorIndex < myTags.size())
159 {
160 // Found the tag in the hash. So, update the tag if it
161 // is not the key.
162 if(myKeyTag != tag)
163 {
164 // Not the key, so update the tag.
165 // If the new value is null and the old one is not, decrement the
166 // number of active tags.
167 if((value[0] == 0) && ((myTags[vectorIndex]->getValue())[0] != 0))
168 {
169 // Tag was deleted since the new value is blank but the old
170 // value was not.
171 --myNumActiveTags;
172 }
173 else if((value[0] != 0) &&
174 ((myTags[vectorIndex]->getValue())[0] == 0))
175 {
176 // Tag was added since the old value was blank and the new value
177 // is not.
178 ++myNumActiveTags;
179 }
180
181 // Just modifying a tag, so this does not affect the number
182 // of active tags.
183 return(myTags[vectorIndex]->setValue(value));
184 }
185 else if(strcmp(value, myTags[vectorIndex]->getValue()) == 0)
186 {
187 // The new key value is the same as the previous value, so
188 // it is not a change, return true.
189 return(true);
190 }
191 else
192 {
193 // Can't modify the key tag's value since that will
194 // screw up the hash.
195 std::cerr << "Can't modify the key tag, " << tag << " from "
196 << myTags[vectorIndex]->getValue() << " to "
197 << value << std::endl;
198 return(false);
199 }
200 }
201
202 // Got an invalid index from the hash. This is not supposed to happen.
203 // so return false.
204 std::cerr << "Invalid tag index found: " << vectorIndex
205 << ", but max index is " << myTags.size() << " for tag: "
206 << tag << std::endl;
207 return(false);
208}
209
210
211// Reset this header record to an empty state.
213{
214 // Delete the tag hash.
215 myTagHash.Clear();
216
217 // Loop through deleting all the tags in the vector.
218 for(unsigned int vectorIndex = 0;
219 vectorIndex < myTags.size();
220 vectorIndex++)
221 {
222 delete myTags[vectorIndex];
223 myTags[vectorIndex] = NULL;
224 }
225 // Clear the tag vector.
226 myTags.clear();
227
228 myNumActiveTags = 0;
229}
230
231
232// Appends the string representation of this header record
233// to the passed in string.
234bool SamHeaderRecord::appendString(std::string& header)
235{
236 // Track whether or not the header type has been written.
237 // Only write the header type if at least one of the tags has
238 // an associated value.
239 bool writtenHeader = false;
240
242 {
243 // Loop through all the entries in the tag vector.
244 for(unsigned int vectorIndex = 0;
245 vectorIndex < myTags.size();
246 vectorIndex++)
247 {
248 if(!writtenHeader && (myTags[vectorIndex]->hasValue()))
249 {
250 // The tag has a value and the header type has not yet been written,
251 // so write it.
252 header += "@";
253 header += myTypeString;
254 writtenHeader = true;
255 }
256 myTags[vectorIndex]->getTagString(header);
257 }
258
259 // If a header has been written, add a new line character.
260 if(writtenHeader)
261 {
262 header += "\n";
263 return(true);
264 }
265 }
266
267 // Nothing was written, return false.
268 return(false);
269}
270
271
272// Add the key tag with the specified value.
273bool SamHeaderRecord::addKey(const char* value)
274{
275 if(myKeyTag.size() == 0)
276 {
277 return(false);
278 }
279 return(setTag(myKeyTag.data(), value));
280}
281
282
283// Return the value associated with the specified tag.
285{
286 // Look up the tag in myTags.
287 int index = myTagHash.Integer(myKeyTag.c_str());
288 if(index < 0)
289 {
290 // The tag was not found in the hash, so return "".
291 return("");
292 }
293
294 // The tag was found in the hash, so return the tag value found at the
295 // index associated with the tag.
296 return(myTags[index]->getValue());
297}
298
299
300// This header is active if there is at least one tag set.
302{
303 return(myNumActiveTags != 0);
304}
305
306
307// Return the type of this header record.
309{
310 return(myTypeString.c_str());
311}
312
313
314// Return the type of this header record.
316{
317 return(myType);
318}
319
320
321void SamHeaderRecord::addRequiredTag(const char* requiredTag)
322{
323 myRequiredTags.push_back(requiredTag);
324}
325
326
327void SamHeaderRecord::internalCopy(SamHeaderRecord& newRec) const
328{
329 newRec.myTagHash = myTagHash;
330
331 newRec.myTags.clear();
332
333 // Loop through copying the tags.
334 for(unsigned int vectorIndex = 0;
335 vectorIndex < myTags.size();
336 vectorIndex++)
337 {
338 if(myTags[vectorIndex] != NULL)
339 {
340 newRec.myTags.push_back(new SamHeaderTag(*(myTags[vectorIndex])));
341 }
342 }
343 newRec.myRequiredTags = myRequiredTags;
344 newRec.myNumActiveTags = myNumActiveTags;
345}
This class encapsulates the tag value pairs contained with a SAM Header line with accessors for getti...
const char * getKeyValue() const
Get the value associated with the key tag. Returns "" if it is not set.
const char * getTagValue(const char *tag) const
Return the value associated with the specified tag.
const char * getTypeString()
Return the type of this header record (HD, SQ, RG, or PG) as a string.
void reset()
Reset this header record to an empty state with no tags.
SamHeaderRecordType getType()
Return the type of this header record (HD, SQ, RG, or PG) as an enum.
virtual ~SamHeaderRecord()
Destructor.
bool isValid()
Check to see if the record is valid.
bool setFields(const StringArray &tokens)
Set the fields from the passed in line.
bool isActiveHeaderRecord()
This record is active (true) if there is at least one tag set.
bool appendString(std::string &header)
Appends the string representation of this header record to the passed in string.
bool addKey(const char *value)
Add the key tag with the specified value (not for HD headers).
SamHeaderRecordType
Specifies the Type for the sam header record (line).
SamHeaderRecord()
Constructor.
bool setTag(const char *tag, const char *value)
Set the value of the specified tag to the specified value, deletes the tag when value is NULL.