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COMBINE-lab / RapMap

Rapid sensitive and accurate read mapping via quasi-mapping
GNU General Public License v3.0
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Empty reads cause premature termination #19

Closed roryk closed 8 years ago

roryk commented 8 years ago

Hi Rob,

Empty reads cause RapMap to skip the rest of the file, for example:

https://dl.dropboxusercontent.com/u/2822886/rapmap-test.fq

with

./rapmap pseudomap -r rapmap-test.fq -i transcriptome/hg19_ERCC92

reports 0 reads. It looks like the jellyfish parser just checks to see if it has received any input, and not for the end of the file. My c++ kung fu is weak so I couldn't figure out a good fix.

rob-p commented 8 years ago

Thanks for reporting this. I'll mention it upstream in the Jellyfish repo, as I'm sure Guillaume would be interested in knowing about this and fixing it.

rob-p commented 8 years ago

Hi @roryk — I've pushed this change in the quasi-mph branch. Can you grab this branch and make sure that it properly handles this input on your end. If you're working in the same directory as before, you'll want to make sure that all remnants of the old jellyfish and cmake cache files are cleared out.

roryk commented 8 years ago

Thanks Rob, sorry to be a pain in the neck. It looks like something got included in libdivsufsort that shouldn't have:

[ 16%] Performing download step (verify and extract) for 'libdivsufsort'
cd /groups/bcbio/singlecell-test/allon/rerun/RapMap/external && /usr/local/bin/cmake -P /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/libdivsufsort-prefix/src/libdivsufsort-stamp/verify-libdivsufsort.cmake
-- verifying file...
     file='/groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
cd /groups/bcbio/singlecell-test/allon/rerun/RapMap/external && /usr/local/bin/cmake -P /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/libdivsufsort-prefix/src/libdivsufsort-stamp/extract-libdivsufsort.cmake
-- extracting...
     src='/groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort.tar.gz'
     dst='/groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
cd /groups/bcbio/singlecell-test/allon/rerun/RapMap/external && /usr/local/bin/cmake -E touch /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/libdivsufsort-prefix/src/libdivsufsort-stamp/libdivsufsort-download
/usr/local/bin/cmake -E cmake_progress_report /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/CMakeFiles 14
[ 18%] No patch step for 'libdivsufsort'
/usr/local/bin/cmake -E touch /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/libdivsufsort-prefix/src/libdivsufsort-stamp/libdivsufsort-patch
/usr/local/bin/cmake -E cmake_progress_report /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/CMakeFiles 13
[ 20%] Performing update step for 'libdivsufsort'
cd /groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master && sh -c "mkdir -p /groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master/build"
cd /groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master && /usr/local/bin/cmake -E touch /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/libdivsufsort-prefix/src/libdivsufsort-stamp/libdivsufsort-update
/usr/local/bin/cmake -E cmake_progress_report /groups/bcbio/singlecell-test/allon/rerun/RapMap/build/CMakeFiles 15
[ 21%] Performing configure step for 'libdivsufsort'
cd /groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master/build && /usr/local/bin/cmake -DCMAKE_INSTALL_PREFIX:PATH=/groups/bcbio/singlecell-test/allon/rerun/RapMap/external/install -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE "-GUnix Makefiles" /groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master
CMake Error: The current CMakeCache.txt directory /groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master/build/CMakeCache.txt is different than the directory /home/rob/RapMap/external/libdivsufsort-master/build where CMakeCache.txt was created. This may result in binaries being created in the wrong place. If you are not sure, reedit the CMakeCache.txt
CMake Error: The source "/groups/bcbio/singlecell-test/allon/rerun/RapMap/external/libdivsufsort-master/CMakeLists.txt" does not match the source "/home/rob/RapMap/external/libdivsufsort-master/CMakeLists.txt" used to generate cache.  Re-run cmake with a different source directory.
make[2]: *** [libdivsufsort-prefix/src/libdivsufsort-stamp/libdivsufsort-configure] Error 1
make[2]: Leaving directory `/groups/bcbio/singlecell-test/allon/rerun/RapMap/build'
make[1]: *** [CMakeFiles/libdivsufsort.dir/all] Error 2
make[1]: Leaving directory `/groups/bcbio/singlecell-test/allon/rerun/RapMap/build'
rob-p commented 8 years ago

Sorry about that; this should be fixed now.