How to estimate the memory use (-Xmx?G) when using FilterSamReads? I always get the errors:
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.regex.Pattern$Start.(Pattern.java:3450)
at java.util.regex.Pattern.compile(Pattern.java:1716)
at java.util.regex.Pattern.(Pattern.java:1351)
at java.util.regex.Pattern.compile(Pattern.java:1028)
at java.lang.String.split(String.java:2380)
at java.lang.String.split(String.java:2422)
at htsjdk.samtools.filter.ReadNameFilter.(ReadNameFilter.java:58)
at picard.sam.FilterSamReads.doWork(FilterSamReads.java:233)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
