Tribble parsing error message

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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Tribble parsing error message #1462

Closed jrobinso closed 4 years ago

jrobinso commented 4 years ago

Parsing errors in Tribble result in the following error message

Error parsing line at byte position: LineIteratorImpl(SynchronousLineReader), for input source: /Users/jrobinso/Downloads/ARHI0A_peaks_std_500.bed

This is not helpful, and even if the "byte position" were displayed it would be only slightly more helpful. I think either the line number, or the text of the line itself, should be displayed.

This is related but more narrow than https://github.com/samtools/htsjdk/issues/709

jrobinso commented 4 years ago

Thanks @yfarjoun , this is a big improvement!

yfarjoun commented 4 years ago

my pleasure! anything we can do for our most visible user!

lbergelson commented 4 years ago

@yfarjoun I noticed after the fact, there's another nearly identical error message in the QueryingIterator directly below this one. Maybe we should update that too?