Picard release 1.115
- EstimateLibraryComplexity: Control size of sorting collection with
MAX_RECORDS_IN_RAM
- Adds COMPRESS_OUTPUTS parameter to IlluminaBasecallsToFastq so that it can
generate compressed FASTQ files (with file extension .fastq.gz). Default is
false.
- SamToFastq: Clarify what a "non-PF read" is.
- Avoid logging a NullPointerException if IlluminaBasecallsToFastq is started
with FORCE_GC=false. GC timer write to the 'log' instead of directly to
System.out. There is really no reason to handle this information differently
than other logging.
- Adds BARCODES_DIR parameter to IlluminaBasecallsToFastq and
IlluminaBasecallsToSam so that they can use the barcode files from
ExtractIlluminaBarcodes when it has been run with OUTPUT_DIR different from the
BASECALLS_DIR parameter. The use case is that the BASECALLS_DIR directory is
read-only and the barcode files can't be written to that directory and the
other tools are useless if they can't read the barcode files from a different
directory.
- Remove bzip2 classes from non-executable picard-<version>.jar
- MarkDuplicates: Indicate in INPUT doc string that it may not be streamed.
- Remove dependence on JAVA6_HOME environment variable.
- Use a StringBuffer instead of synchronization when generating log messages.
The only exception is if the stacktrace of a Throwable also needs to be
written. Then we have to ensure that our message goes with the stacktrace so we
need synchronization there. But this should not be a drawback since the
Throwable.printStackTrace() itself synchronizes on the PrintStream.
- Synchronize on the 'out' PrintStream instead of 'this' to avoid mixing up log
statements from different threads.
- Use the same buffer as the rest of htslib in the reference sequence / fasta
file classes.
- FastqRecord: added methods equals, hashcode, toString, length
- Detect old style metric file and skip over header reading code.
- Add additional boolean genotype functions to JEXLMap to add functionality to
GATK tools using JEXL (like VariantFiltration)
- Case of symbolic allele ID string now being preserved as per VCFv4.1 section
1.4.5
- BAM query optimization: Don't iterate over bins that are not actually
interesting
- Fix nullpointer exception when BAMFileSpan is null
- IntervalTreeMap: added two methods to test interval overlapping
- Add reference sequence index cache to speed up query by 20% for certain
usecases
- VariantContextBuilder: no longer crashing when an attribute is set without
loading attributes or explicitly calling .attributes(null) first
- Accepting VCF 4.2 breakend and inline symbolic insertion alleles
- Better message when reference fasta index does not exist.
- AbstractBAMFileIndex.java: 40% speed improvement for query under certain
workloads
-Alec
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