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package driver;
public class MakeTestScriptScoreOnly {
public static void main(String[] args){
assert(args.length==1) : "Please enter number of reads.";
numReads=Integer.parseInt(args[0]);
// String[] strings=new String[] {
// "/work/bbushnell/ssaha2/ssaha2 -solexa -outfile #S.sam -best -1 -output sam_soft -save hg37 " +
// "/work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime defaultTime.txt",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S.sam #R ssaha2",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime defaultTime.txt"
// };
// String[] strings=new String[] {
// "bwa aln -t 22 bs_ /work/bbushnell/synth/reads_B1_100000x100bp_#S_chr1-25.fq > temp_default.sai",
// "bwa samse bs_ temp_default.sai /work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq > #S_default.sam",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime defaultTime.txt",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S_default.sam #R",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime defaultTime.txt"
// };
// String[] strings=new String[] {
// "java -ea -Xms24g -Xmx31g -server -XX:+UseNUMA -XX:+AggressiveOpts -XX:+UseCompressedOops " +
// "align.TestIndex11f 1 25 100 0 /work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq null " +
// "outfile=#S_bbmap11f.sam cs=false threads=22 paired=false pairlen=100 build=37 match=short " +
// "removeambiguous=false fastqparsecustom overwrite savepar=false",
//
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime bbmap11fTime.txt",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S_bbmap11f.sam #R",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime bbmap11fTime.txt"
// };
// String[] strings=new String[] {
// "bowtie --best -y --chunkmbs 1024 --strata -m 1 -k 2 -v 3 -p 24 -t -q -S HG37" +
// " /work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq #S_bowtie.sam",
//
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime bowtieTime.txt",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S_bowtie.sam #R",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime bowtieTime.txt"
// };
// String[] strings=new String[] {
// "bfast match -T $TMPDIR/ -n 16 -f hg19.fa -r /work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq > $TMPDIR/#S.bmf",
// "bfast localalign -n 16 -f hg19.fa -m $TMPDIR/#S.bmf > $TMPDIR/#S.baf",
//// "bfast postprocess -n 16 -a 3 -f hg19.fa -i $TMPDIR/#S.baf > #S.sam",
//// "bfast postprocess -n 16 -a 3 -m 20 -f hg19.fa -i $TMPDIR/#S.baf > #S_r#R.sam",
// "bfast postprocess -n 16 -M 20 -f hg19.fa -i $TMPDIR/#S.baf > #S_r#R.sam",
//
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime bfastTime.txt",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S_r#R.sam #R",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime bfastTime.txt"
// };
// String[] strings=new String[] {
// "smalt_x86_64 map -n 8 -a -f samsoft -o #S_r#R.sam hg37 /work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime mapTime.txt",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S_r#R.sam #R ssaha2",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime mapTime.txt",
// };
// String[] strings=new String[] {
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime mapTime.txt",
// "./soap -p 24 -a /work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq -D hg37.fa.index -o #S_r#R.soap",
// "perl soap2sam.pl -p #S_r#R.soap > #S_r#R.sam",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime mapTime.txt",
// "java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S_r#R.sam #R",
// };
String[] strings=new String[] {
"java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime mapTime.txt",
"./bin/gmapper-ls /work/bbushnell/synth/reads_B1_#Rx100bp_#S_chr1-25.fq --single-best-mapping --qv-offset 33 -L hg37 -N 24 -o 5 -h 80% > #S_r#R.sam",
"java -ea -Xmx96m -cp /work/bbushnell/java/ align.PrintTime mapTime.txt",
"java -ea -Xmx96m -cp /work/bbushnell/java/ align.GradeSamFile #S_r#R.sam #R",
};
int[] blank=new int[] {0, 0, 0, 0};
print(strings, blank, 100);
print(strings, blank, 100);
print(strings, blank, 100);
print(strings, blank, 100);
for(int[] array : sets){
print(strings, array, numReads);
}
}
private static void print(String[] array, int[] blank, int x) {
String counts=(blank[0]+"S_"+blank[1]+"I_"+blank[2]+"D_"+blank[3]+"U");
String reads=""+x;
for(String s : array){
String s2=s.replaceAll("#S", counts).replaceAll("#R", reads);
System.out.println(s2);
}
System.out.println();
}
public static int numReads=400000;
public static final int[][] sets=new int[][] {
{0, 0, 0, 0},
{1, 0, 0, 0},
{2, 0, 0, 0},
{3, 0, 0, 0},
{4, 0, 0, 0},
{5, 0, 0, 0},
{6, 0, 0, 0},
{7, 0, 0, 0},
{8, 0, 0, 0},
{10, 0, 0, 0},
{12, 0, 0, 0},
{14, 0, 0, 0},
{16, 0, 0, 0},
{18, 0, 0, 0},
{20, 0, 0, 0},
{24, 0, 0, 0},
{28, 0, 0, 0},
{32, 0, 0, 0},
{36, 0, 0, 0},
{40, 0, 0, 0},
{0, 1, 0, 0},
{0, 2, 0, 0},
{0, 3, 0, 0},
{0, 4, 0, 0},
{0, 5, 0, 0},
{0, 6, 0, 0},
{0, 7, 0, 0},
{0, 8, 0, 0},
{0, 10, 0, 0},
{0, 12, 0, 0},
{0, 14, 0, 0},
{0, 16, 0, 0},
{0, 20, 0, 0},
{0, 24, 0, 0},
{0, 28, 0, 0},
{0, 32, 0, 0},
{0, 36, 0, 0},
{0, 40, 0, 0},
{0, 0, 1, 0},
{0, 0, 2, 0},
{0, 0, 3, 0},
{0, 0, 4, 0},
{0, 0, 5, 0},
{0, 0, 6, 0},
{0, 0, 7, 0},
{0, 0, 8, 0},
{0, 0, 10, 0},
{0, 0, 12, 0},
{0, 0, 14, 0},
{0, 0, 16, 0},
{0, 0, 20, 0},
{0, 0, 24, 0},
{0, 0, 28, 0},
{0, 0, 32, 0},
{0, 0, 48, 0},
{0, 0, 64, 0},
{0, 0, 128, 0},
{0, 0, 192, 0},
{0, 0, 256, 0},
{0, 0, 512, 0},
{0, 0, 1000, 0},
{0, 0, 2000, 0},
{0, 0, 3000, 0},
{0, 0, 4000, 0},
{0, 0, 6000, 0},
{0, 0, 8000, 0},
{0, 0, 10000, 0},
{0, 0, 12000, 0},
{0, 0, 14000, 0},
{0, 0, 16000, 0},
{0, 0, 20000, 0},
{0, 0, 24000, 0},
{0, 0, 28000, 0},
{0, 0, 32000, 0},
{0, 0, 0, 1},
{0, 0, 0, 2},
{0, 0, 0, 3},
{0, 0, 0, 4},
{0, 0, 0, 5},
{0, 0, 0, 6},
{0, 0, 0, 7},
{0, 0, 0, 8},
{0, 0, 0, 10},
{0, 0, 0, 12},
{0, 0, 0, 14},
{0, 0, 0, 16},
{0, 0, 0, 20},
{0, 0, 0, 24},
{0, 0, 0, 28},
{0, 0, 0, 32},
{0, 0, 0, 36},
{0, 0, 0, 40}
};
}
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