Fastq reader clips long reads at 10,000 bp

[heuermh]

E.g. ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/

$ dsh-bio fastq-sequence-length -i combined_2018-05-18.fastq.gz | sort -n -r | head
322099
298433
283861
262525
247501

scala> val reads = sc.loadAlignments("combined_2018-05-18.fastq.gz")
reads: org.bdgenomics.adam.rdd.read.AlignmentRecordRDD =
ParquetUnboundAlignmentRecordRDD with 0 reference sequences, 0 read groups,
and 0 processing steps

scala> val lengths = reads.rdd.map(_.sequence.length()).collect()
lengths: Array[Int] = Array(641, 3082, 10000, 10000, 10000, ...

scala> lengths.sortBy(-1 * _).take(10)
res3: Array[Int] = Array(10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, ...