zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Be explicitly clear about which options are for debugging purposes only and shouldn't be used if your username is not ebanks@broad. If only we had a @hidden annotation option for args... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3909 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-30 14:18:31 +00:00
parent ac8048f17b
commit 6d91cd587e
1 changed files with 11 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -85,15 +85,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// ADVANCED OPTIONS FOLLOW
@Argument(fullName="outputIndels", shortName="indels", required=false, doc="Output file (text) for the indels found")
protected String OUT_INDELS = null;
@Argument(fullName="statisticsFile", shortName="stats", doc="print out statistics (what does or doesn't get cleaned)", required=false)
protected String OUT_STATS = null;
@Argument(fullName="SNPsFile", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out", required=false)
protected String OUT_SNPS = null;
@Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false)
protected int MAX_CONSENSUSES = 30;
@ -119,6 +110,17 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="targetIntervalsAreNotSorted", shortName="targetNotSorted", required=false, doc="This tool assumes that the target interval list is sorted; if the list turns out to be unsorted, it will throw an exception. Use this argument when your interval list is not sorted to instruct the Realigner to first sort it in memory.")
protected boolean TARGET_NOT_SORTED = false;
// DEBUGGING OPTIONS FOLLOW
@Argument(fullName="indelsFileForDebugging", shortName="indels", required=false, doc="Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY")
protected String OUT_INDELS = null;
@Argument(fullName="statisticsFileForDebugging", shortName="stats", doc="print out statistics (what does or doesn't get cleaned); FOR DEBUGGING PURPOSES ONLY", required=false)
protected String OUT_STATS = null;
@Argument(fullName="SNPsFileForDebugging", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out; FOR DEBUGGING PURPOSES ONLY", required=false)
protected String OUT_SNPS = null;
// the intervals input by the user
private Iterator<GenomeLoc> intervals = null;