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Minor fixes to the cmd-line help messages 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5470 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-03-18 18:18:04 +00:00
parent 7857cb5a22
commit 1d5326ff0c
1 changed files with 10 additions and 7 deletions
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17
java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java
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@ -52,13 +52,15 @@ import net.sf.samtools.SAMFileReader.ValidationStringency;
public class RemapAlignments extends CommandLineProgram {
// Usage and parameters
@Usage(programVersion="1.0") public String USAGE = "Investigates indels called in the alignment data\n";
@Usage(programVersion="1.0") public String USAGE = "Remaps custom-reference (e.g. transcriptome) alignments onto the genomic reference\n";
@Option(shortName="M",
doc="Map file: from the reference the reads were aligned to, to the master reference the alignments should be remapped to",
doc="Map file: from the reference the reads were aligned to, to the master reference the alignments should be remapped to. "+
"In other words, for each custom-reference contig C this map must provide a (possibly disjoint) list of intervals "+
"on the target reference, onto which C maps base-by-base. ",
optional=false)
public File MAP_FILE = null;
@Option(shortName="I",
doc="Input file (bam or sam) with alignments to be remapped",
doc="Input file (bam or sam) with alignments to be remapped",
optional=false)
public File IN = null;
@Option(shortName="O",
@ -66,14 +68,15 @@ public class RemapAlignments extends CommandLineProgram {
optional=false)
public File OUT = null;
@Option(shortName="R",
doc="Reference to remap alignments onto.",
doc="Target reference to remap alignments onto.",
optional=false)
public File REFERENCE = null;
@Option(
doc="If a read has multiple alignments that are exactly the same after remapping, "+
"keep only one copy of such alignment in output file. Multiple alignments that are "+
"not equivalent after remaping are not affected by this flag. "+
"Multiple alignments for the same query must be grouped on adjacent lines of the input file to be detected," +
"then keep only one copy of such alignment in output file. Multiple alignments that are "+
"not equivalent after remapping are not affected by this flag. "+
"Multiple alignments for the same query must be grouped on adjacent lines of the input file to be detected "+
"(i.e. input file must be sorted by read name), " +
"otherwise REDUCE will have no effect.",
optional=true)
public boolean REDUCE = false;