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

Updating docs to include more details

This commit is contained in:
Eric Banks 2011-09-15 16:25:03 -04:00
parent 6d02a34bfb
commit fd1831b4a5
2 changed files with 7 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
View File

@ -43,8 +43,10 @@ import java.util.List;
* Generates an alternative reference sequence over the specified interval.
*
* <p>
* Given variant ROD tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
* Additionally, allows for a "snpmask" ROD to set overlapping bases to 'N'.
* Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
* Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.
* Note that if there are multiple variants at a site, it takes the first one seen.
* Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
*
* <h2>Input</h2>
* <p>

3
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
View File

@ -42,6 +42,9 @@ import java.io.PrintStream;
*
* <p>
* The output format can be partially controlled using the provided command-line arguments.
* Specify intervals with the usual -L argument to output only the reference bases within your intervals.
* Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a
* separate fasta sequence (named numerically in order).
*
* <h2>Input</h2>
* <p>