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[ADAM-1481] Refactor ADAMContext loadXxx methods for consistency #1487

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merged 8 commits into from Apr 19, 2017
Merged

[ADAM-1481] Refactor ADAMContext loadXxx methods for consistency #1487

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b0505c4
Refactor ADAMContext loadXxx methods for consistency, commit 1 of sev…
heuermh Apr 12, 2017
7e6bca7
Format long lines
heuermh Apr 12, 2017
f894f8a
Minor doc fixes
heuermh Apr 13, 2017
6c988b7
Add FileExtensions, confirm pathName doc strings
heuermh Apr 13, 2017
c7814c9
Missed merge flotsam
heuermh Apr 14, 2017
f3d1d3c
Moar doc fixes, add'l load methods
heuermh Apr 14, 2017
b021e2c
Use compression codecs from Hadoop configuration instead of hardcoded…
heuermh Apr 18, 2017
9b13e6e
Document compressed file support via Hadoop compression codecs.
heuermh Apr 19, 2017
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19 changes: 11 additions & 8 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
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Expand Up @@ -165,7 +165,8 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
}

/**
* @param pathName The (possibly globbed) path to load a VCF from.
* @param pathName The path name to load VCF format metadata from.
* Globs/directories are supported.
* @return Returns a tuple of metadata from the VCF header, including the
* sequence dictionary and a list of the samples contained in the VCF.
*/
Expand All @@ -180,7 +181,8 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
}

/**
* @param pathName The (possibly globbed) path to load a VCF from.
* @param pathName The path name to load VCF format metadata from.
* Globs/directories are supported.
* @return Returns a tuple of metadata from the VCF header, including the
* sequence dictionary and a list of the samples contained in the VCF.
*
Expand Down Expand Up @@ -492,10 +494,11 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
* the reads from a fragment in a single split. This allows us to eliminate
* an expensive groupBy when loading a BAM file as fragments.
*
* @param pathName The path name to load reads from. Globs/directories are
* supported.
* @param stringency The validation stringency to use when reading the header.
* @return Returns true if all files described by the filepath are queryname
* @param pathName The path name to load SAM/BAM/CRAM formatted alignment records from.
* Globs/directories are supported (todo: confirm).
* @param stringency The validation stringency to use when validating the
* SAM/BAM/CRAM format header. Defaults to ValidationStringency.STRICT.
* @return Returns true if all files described by the path name are queryname
* sorted.
*/
private[rdd] def filesAreQuerynameSorted(
Expand Down Expand Up @@ -536,8 +539,8 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
* header. SAMRecords are read from the file and converted to the
* AlignmentRecord schema.
*
* @param pathName The path name to load SAM/BAM/CRAM formatted alignments from. Globs/directories are
* supported (todo: confirm).
* @param pathName The path name to load SAM/BAM/CRAM formatted alignment records from.
* Globs/directories are supported (todo: confirm).
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Can confirm; globs/directories are supported.

* @return Returns an AlignmentRecordRDD which wraps the RDD of alignment records,
* sequence dictionary representing contigs the alignment records may be aligned to,
* and the record group dictionary for the alignment records if one is available.
Expand Down