= "Usage: AnnotationUtils TASK=<task_num> <task_args>\n" +
"\tTasks:\n" +
"\t\t1. Take the intersection two annotation sets: -set1 <File containing first set> -set2 <File containing second set> -minScore <to filter by minimum annotation score>" +
"\n\t\t\t [-set1format <[BED], GFF or generic> -set2format <[BED], GFF or generic> -outformat <desired output format BED, GFF or generic, default is se1format>" +
"\n\t2. Take the difference of two annotation sets (all annotations in set1 that do not overlap set2): -set1 <File containing first set> -set2 <File containing second set> -minScore <to filter by minimum annotation score>" +
"\n\t\t [-set1format <[BED], GFF or generic> -set2format <[BED], GFF or generic> -outformat <desired output format BED, GFF or generic, default is se1format>" +
"\n\t3. Print out all elements in one set (set1) that overlap another (set2): -set1 <File containing first set> -set2 <File containing second set> " +
"\n\t\t [-set1format <[BED], GFF or generic> -set2format <[BED], GFF or generic> -outformat <desired output format BED, GFF or generic, default is se1format>" +
"\n\t4. Merge annotation file -in <annotation file (dowa not support standard input input at this point)> -out <output file name or standard output by default> [-format <[BED], GFF or generic>]" +
"\n\t5. Reformat annotation file -in <annotation file (dowa not support standard input input at this point)> -out <output file name or standard output by default> [-informat <[BED], GFF or generic> -outformat <BED,[GFF],generic]" +
"\n\t6. Shuffle scores -in <Annotation file> -out <output file name or standard output by default> [-informat <[BED], GFF or generic>]" +
"\n\t7. Get overlap statistics of two sets (how much each of the elements in set1 is covered by set2). " +
"\n\t\t [-set1format <[BED], GFF or generic> -set2format <[BED], GFF or generic> -outformat <desired output format BED, GFF or generic, default is se1format>" +
"\n\t8. Take the complement of the the first annotation set in the second set (similar to 2 but elements incompletely overlapping will be broken into the regions that don't overlap): -set1 <File containing first set> -set2 <File containing second set> " +
"\n\t9. Filter any delimited file by extracting all records that overlap a given annotation file -in <Delimted file> -chrColumn <Column containing chrmosome information (first column is 0)> [-chr <Alternative if there is no chromosome information in the file, it is assumed that all positions are in a given chromosome>] -positionColumn <Column containing position information (first column is 0)> -annotations <Annotation file> -annotationFormat <[BED], GFF, Generic> [-sepeartor <Character separting columns, tab is assumed by default>]"+
"\n\t10. Print out all elements in one set (set1) that overlap another (set2) and are in the same orientation as the overlapping gene: -set1 <File containing first set> -set2 <File containing second set> " +
"\n\t\t [-set1format <[BED], GFF or generic> -set2format <[BED], GFF or generic> -outformat <desired output format BED, GFF or generic, default is se1format>" +
"\n\t11. Compute the probability that an interval of given size overlaps a given annotation set by chance: -set <File containing first set> -sizeFile <Size file with chromosome sizes> " +
"\n\t12. Print distance metrics: for each element in first set, print the distance to the closest element in the second set." +
"\n\t\t [-nonOverlapping <find the closest non-overlapping element> -set1format <[BED], GFF or generic> -set2format <[BED], GFF or generic> -chr <limit analysis to chr>" +
"\n\tSlideAndCount\tSlide a window over the annotation map and count elements that overlap each window" +
"\n\t\t -window <windowSize> -overlap <overlapSize> -chr <chr> -start <start> -end <end>" +
"\n\tOverlapSignifiance. Calculate the significance of the overlap between two sets of annotations by permuting across the same chromosome." +
"\n\t\t -set1 <set1> -set2 <set2> -nperm <number of permutations> -sizeFile <file of chromosome sizes>" +
"\n"
1.8.7
