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[ADAM-1456] Remove .{type}.adam file extension conversions in type-guessing methods. #1482

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Apr 13, 2017
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[ADAM-1456] Remove .{type}.adam file extension conversions in type-guessing methods. #1482

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17 changes: 5 additions & 12 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -1496,7 +1496,6 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
* * SAM/BAM/CRAM (.sam, .bam, .cram)
* * FASTQ (interleaved, single end, paired end) (.ifq, .fq/.fastq)
* * FASTA (.fa, .fasta)
* * NucleotideContigFragments via Parquet (.contig.adam)
*
* As hinted above, the input type is inferred from the file path extension.
*
Expand All @@ -1507,7 +1506,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
* @param recordGroupOpt Optional record group name to set if loading FASTQ.
* @param stringency Validation stringency used on FASTQ import/merging.
* @return Returns an AlignmentRecordRDD which wraps the RDD of reads,
* sequence dictionary representing the contigs these reads are aligned to
* the sequence dictionary representing the contigs these reads are aligned to
* if the reads are aligned, and the record group dictionary for the reads
* if one is available.
* @see loadBam
Expand Down Expand Up @@ -1539,11 +1538,8 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
filePath.endsWith(".fasta")) {
log.info(s"Loading $filePath as FASTA and converting to AlignmentRecords. Projection is ignored.")
AlignmentRecordRDD.unaligned(loadFasta(filePath, fragmentLength = 10000).toReads)
} else if (filePath.endsWith("contig.adam")) {
log.info(s"Loading $filePath as Parquet of NucleotideContigFragment and converting to AlignmentRecords. Projection is ignored.")
AlignmentRecordRDD.unaligned(loadParquetContigFragments(filePath).toReads)
} else {
log.info(s"Loading $filePath as Parquet of AlignmentRecords.")
log.info(s"Loading $filePath as Parquet containing AlignmentRecords.")
loadParquetAlignments(filePath, None, projection)
}
}
Expand All @@ -1555,8 +1551,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
*
* * Fragments via Parquet (default)
* * SAM/BAM/CRAM (.sam, .bam, .cram)
* * FASTQ (interleaved only --> .ifq)
* * Autodetects AlignmentRecord as Parquet with .reads.adam extension.
* * FASTQ (interleaved only, .ifq)
*
* @param filePath Path to load data from.
* @return Returns the loaded data as a FragmentRDD.
Expand All @@ -1575,13 +1570,11 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
log.info(s"Loading $filePath as SAM/BAM and converting to Fragments.")
loadBam(filePath).toFragments
}
} else if (filePath.endsWith(".reads.adam")) {
log.info(s"Loading $filePath as ADAM AlignmentRecords and converting to Fragments.")
loadAlignments(filePath).toFragments
} else if (filePath.endsWith(".ifq")) {
log.info("Loading interleaved FASTQ " + filePath + " and converting to Fragments.")
log.info(s"Loading $filePath as interleaved FASTQ and converting to Fragments.")
loadInterleavedFastqAsFragments(filePath)
} else {
log.info(s"Loading $filePath as Parquet containing Fragments.")
loadParquetFragments(filePath)
}
}
Expand Down