Sam file from stdin

[Jelinek-J]

Hi,

it is possible to read fastq file from standard input using zcat test.fastq.gz | fastqc stdin. However I'm not able to read bam/ sam file from standard input this way (useful e.g. if there are multialignments) samtools view -F 256 -h test.bam | fastqc stdin produces a following error:

null
Failed to process stdin
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline '@SQ    SN:ENST00000000001      LN:1000' didn't start with '+' at 3
        at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:179)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:93)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:163)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:125)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)

Apparently automatic file format detection does not work with standard input and it tries to parse it as a fastq file. But forcing the correct format (samtools view -F 256 -h test.bam | fastqc -f sam stdin) will just produce a different error.:

Failed to process stdin
java.io.FileNotFoundException: stdin (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:213)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:152)
        at uk.ac.babraham.FastQC.Sequence.BAMFile.<init>(BAMFile.java:62)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:81)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:163)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:125)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)

So it looks like specifying the format turns off the special handling of the 'stdin' keyword.

$ fastqc -v
FastQC v0.12.1