libStatGen Software  1
ShiftIndels.cpp
1 /*
2  * Copyright (C) 2011 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 "ShiftIndels.h"
19 #include "SamFile.h"
20 
21 void testShiftIndels()
22 {
23  ShiftIndelsTest::testShift("testFiles/testShift.sam", "results/testShift.sam");
24 #ifdef __ZLIB_AVAILABLE__
25  ShiftIndelsTest::testShift("testFiles/testShift.bam", "results/testShift.bam");
26  ShiftIndelsTest::testShift("testFiles/testShift.bam", "results/testShiftFromBam.sam");
27 #endif
28  ShiftIndelsTest::testShift("testFiles/testShift.sam", "results/testShiftFromSam.bam");
29 }
30 
31 void ShiftIndelsTest::testShift(const char* input, const char* output)
32 {
33  SamFile inSam, outSam;
34 
35  assert(inSam.OpenForRead(input));
36  assert(outSam.OpenForWrite(output));
37 
38 
39  // Read the SAM Header.
40  SamFileHeader samHeader;
41  assert(inSam.ReadHeader(samHeader));
42  assert(outSam.WriteHeader(samHeader));
43 
44 
45  SamRecord samRecord;
46  int readNum = 1;
47  bool shiftResult = true;
48  while(inSam.ReadRecord(samHeader, samRecord))
49  {
50  if((readNum == 3)|| (readNum == 5))
51  {
52  shiftResult = false;
53  }
54  else
55  {
56  shiftResult = true;
57  }
58  ++readNum;
59 
60  assert(samRecord.shiftIndelsLeft() == shiftResult);
61  assert(outSam.WriteRecord(samHeader, samRecord));
62  }
63 
64 }
bool ReadHeader(SamFileHeader &header)
Reads the header section from the file and stores it in the passed in header.
Definition: SamFile.cpp:437
Allows the user to easily read/write a SAM/BAM file.
Definition: SamFile.h:35
bool WriteHeader(SamFileHeader &header)
Writes the specified header into the file.
Definition: SamFile.cpp:467
bool WriteRecord(SamFileHeader &header, SamRecord &record)
Writes the specified record into the file.
Definition: SamFile.cpp:619
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:34
bool ReadRecord(SamFileHeader &header, SamRecord &record)
Reads the next record from the file & stores it in the passed in record.
Definition: SamFile.cpp:501
bool OpenForWrite(const char *filename, SamFileHeader *header=NULL)
Open a sam/bam file for writing with the specified filename, determining SAM/BAM from the extension (...
Definition: SamFile.cpp:223
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record...
Definition: SamRecord.h:51
bool OpenForRead(const char *filename, SamFileHeader *header=NULL)
Open a sam/bam file for reading with the specified filename, determing the type of file and SAM/BAM b...
Definition: SamFile.cpp:93