Skip to content

Commit 988600e

Browse files
committed
BBMap updates
1 parent af5a272 commit 988600e

File tree

1 file changed

+5
-5
lines changed

1 file changed

+5
-5
lines changed

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -130,10 +130,10 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
130130
}
131131
}
132132

133-
if (getProvider().getParameterByName("midin").hasValueInJson(getPipelineCtx().getJob(), getProvider(), getStepIdx()))
133+
if (getProvider().getParameterByName("minid").hasValueInJson(getPipelineCtx().getJob(), getProvider(), getStepIdx()))
134134
{
135-
Double val = getProvider().getParameterByName("midin").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Double.class);
136-
params.add("midin=" + val);
135+
Double val = getProvider().getParameterByName("minid").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Double.class);
136+
params.add("minid=" + val);
137137
}
138138

139139
File bam = getWrapper().doAlignment(inputFastq1, inputFastq2, outputDirectory, basename, params);
@@ -186,7 +186,7 @@ public Provider()
186186
{{
187187
put("checked", true);
188188
}}, true),
189-
ToolParameterDescriptor.create("midin", "Minimum Identity", "Approximate minimum alignment identity to look for. Higher is faster and less sensitive", "ldk-numberfield", new JSONObject()
189+
ToolParameterDescriptor.create("minid", "Minimum Identity", "Approximate minimum alignment identity to look for. Higher is faster and less sensitive", "ldk-numberfield", new JSONObject()
190190
{{
191191
put("minValue", 0);
192192
put("maxValue", 1);
@@ -246,7 +246,7 @@ public File doAlignment(File inputFastq1, @Nullable File inputFastq2, File outpu
246246
Integer maxRam = SequencePipelineService.get().getMaxRam();
247247
if (maxRam != null)
248248
{
249-
args.add("-Xmx=" + maxRam + "g");
249+
args.add("-Xmx" + maxRam + "g");
250250
}
251251

252252
Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());

0 commit comments

Comments
 (0)