Bugfix: Make sure lzf filter is properly built

Change port of hdf5server in docker-compose file
to avoid clashing with local java development port.
Use -1 for retrieving all SNPs instead of using the number of accessions
which was calculated anyways wrongly

Dockerfile

@@ -22,7 +22,7 @@ USER root
 WORKDIR /root
 RUN apt update && apt install -y gcc libhdf5-dev git
 RUN git clone https://github.com/h5py/h5py.git
-RUN cd h5py/lzf && gcc -O2 -fPIC -I/usr/include/hdf5/serial -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -lhdf5   -shared lzf/*.c lzf_filter.c -o liblzf_filter.so
+RUN cd h5py/lzf && gcc -O2 -fPIC -I/usr/include/hdf5/serial -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -shared lzf/*.c lzf_filter.c -o liblzf_filter.so -lhdf5 
 
 FROM jetty:9.4.26-jre8
 USER root

docker-compose.yml

@@ -45,7 +45,7 @@ services:
     volumes:
       - /net/gmi.oeaw.ac.at/gwasapp/DATA_NEW_BROWSER/:/mnt
     ports:
-      - 8000:8000
+      - 8001:8000
     environment:
       GWAS_VIEWER_FOLDER: /mnt/gwas_results
       GENOTYPE_FOLDER: /mnt/PYGWAS_GENOTYPES

src/genophenbrowser-server/src/main/java/com/gmi/nordborglab/browser/server/data/hdf5/HDF5GenotypeReader.java

@@ -102,8 +102,6 @@ private int[] getPositions(IHDF5Reader reader, Integer chr, int start, int end)
 
 
     private byte[][] getAlleles(IHDF5Reader reader, Integer chr, Integer start, Integer end, LinkedHashSet<String> passportIds) {
-        HDF5DataSetInformation info = reader.object().getDataSetInformation("snps");
-        final long accessionCount = info.getNumberOfElements();
         List<String> accessionIds = Lists.newArrayList(reader.string().readArray("accessions"));
         List<Integer> passportIndices = Lists.newArrayList();
         // get the indices of the passportIds
@@ -123,7 +121,7 @@ private byte[][] getAlleles(IHDF5Reader reader, Integer chr, Integer start, Inte
         final int end_pos_ix = chr_region[0] + getPositionIndex(positions, end);
         int numberOfSnps = (end_pos_ix - start_pos_ix) + 1;
         // get entire snps
-        final byte[][] snps = reader.int8().readMatrixBlockWithOffset("snps", numberOfSnps, (int) accessionCount, start_pos_ix, 0);
+        final byte[][] snps = reader.int8().readMatrixBlockWithOffset("snps", numberOfSnps, -1, start_pos_ix, 0);
         if (passportIds != null) {
             final byte[][] filteredSNPs = new byte[numberOfSnps][passportIds.size()];
             for (int i = 0; i < filteredSNPs.length; i++) {