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