Irena Hwang

Here are the lines in config.log pertinent to BamReader.h, does this provide more useful information? ``` | #include configure:5231: result: no configure:5231: checking api/BamReader.h presence configure:5231: g++ -E -fopenmp conftest.cpp...

Sure, interestingly I get the same lines in config.log when I use `./configure` as well as `./configure --with-bamtools=~/Programs/bamtools`: ``` configure:5231: checking api/BamReader.h presence configure:5231: g++ -c -std=c++98 -03 -fopenmp conftest.cpp...

Thanks for the suggestion. When I do `./configure --help` I do indeed see the `--with-bamtools` option. Unfortunately, still no dice with the attached configure, whether or not I specify my...

Sure! They're the whole exome files from the GIAB project for Ashkenazim Trio Son (NA24385). The BAM files can be found [here](ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/ion_exome/), which I converted to fastq using samtools for...

Apologies, I thought I had included a link to the exact data files! They can be found here: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/ion_exome/ You're absolutely correct that I forgot to mention using the gzip...

Aha! I'm so used to reading paired-end files. I believe your command is missing the `fastq` argument, however. Unfortunately, now I am receiving a different error: ``` 104953 Floating point...

Huh, it seems to be working today. I did re-run my samtools commands just in case, so maybe I still hadn't been invoking samtools correctly. Thanks for your help!

Also: discussed misspelling of "retrieve" in `datakit data pull to rerieve the data files` with @myersjustinc