1ERROR=false
2
3# Sam To Sam
4../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqNoOpt.sam --noph 2> results/seqNoOpt.sam.log && diff results/seqNoOpt.sam expected/seqOrig.sam && diff results/seqNoOpt.sam.log expected/seq.log \
5&& \
6../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqOrig.sam --noph 2> results/seqOrig.sam.log --useOrigSeq && diff results/seqOrig.sam expected/seqOrig.sam && diff results/seqOrig.sam.log expected/seq.log \
7&& \
8../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqBases.sam --noph 2> results/seqBases.sam.log --useBases && diff results/seqBases.sam expected/seqBases.sam && diff results/seqBases.sam.log expected/seq.log \
9&& \
10../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqEquals.sam --noph 2> results/seqEquals.sam.log --useEquals && diff results/seqEquals.sam expected/seqEquals.sam && diff results/seqEquals.sam.log expected/seq.log \
11&& \
12# Bam to Sam
13../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqNoOptBam.sam --noph 2> results/seqNoOptBam.sam.log && diff results/seqNoOptBam.sam expected/seqOrig.sam && diff results/seqNoOptBam.sam.log expected/seq.log \
14&& \
15../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqOrigBam.sam --noph 2> results/seqOrigBam.sam.log --useOrigSeq && diff results/seqOrigBam.sam expected/seqOrig.sam && diff results/seqOrigBam.sam.log expected/seq.log \
16&& \
17../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqBasesBam.sam --noph 2> results/seqBasesBam.sam.log --useBases && diff results/seqBasesBam.sam expected/seqBases.sam && diff results/seqBasesBam.sam.log expected/seq.log \
18&& \
19../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqEqualsBam.sam --noph 2> results/seqEqualsBam.sam.log --useEquals && diff results/seqEqualsBam.sam expected/seqEquals.sam && diff results/seqEqualsBam.sam.log expected/seq.log \
20&& \
21# Sam To Bam
22../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqNoOpt.bam --noph 2> results/seqNoOpt.bam.log && diff results/seqNoOpt.bam expected/seqOrig.bam && diff results/seqNoOpt.bam.log expected/seq.log \
23&& \
24../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqOrig.bam --noph 2> results/seqOrig.bam.log --useOrigSeq && diff results/seqOrig.bam expected/seqOrig.bam && diff results/seqOrig.bam.log expected/seq.log \
25&& \
26../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqBases.bam --noph 2> results/seqBases.bam.log --useBases && diff results/seqBases.bam expected/seqBases.bam && diff results/seqBases.bam.log expected/seq.log \
27&& \
28../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/seqEquals.bam --noph 2> results/seqEquals.bam.log --useEquals && diff results/seqEquals.bam expected/seqEquals.bam && diff results/seqEquals.bam.log expected/seq.log \
29&& \
30# Bam To Bam
31../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqNoOptBam.bam --noph 2> results/seqNoOptBam.bam.log && diff results/seqNoOptBam.bam expected/seqOrig.bam && diff results/seqNoOptBam.bam.log expected/seq.log \
32&& \
33../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqOrigBam.bam --noph 2> results/seqOrigBam.bam.log --useOrigSeq && diff results/seqOrigBam.bam expected/seqOrig.bam && diff results/seqOrigBam.bam.log expected/seq.log \
34&& \
35../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqBasesBam.bam --noph 2> results/seqBasesBam.bam.log --useBases && diff results/seqBasesBam.bam expected/seqBases.bam && diff results/seqBasesBam.bam.log expected/seq.log \
36&& \
37../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/seqEqualsBam.bam --noph 2> results/seqEqualsBam.bam.log --useEquals && diff results/seqEqualsBam.bam expected/seqEquals.bam && diff results/seqEqualsBam.bam.log expected/seq.log
38
39if [ $? -ne 0 ]
40then
41    ERROR=true
42fi
43
44if($ERROR == true)
45then
46  exit 1
47fi
48
49