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Update utility/; splitHaplotype to new merylExactLookup interface.
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brianwalenz committed Nov 3, 2020
1 parent 604f7fc commit 0b39efc
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Showing 2 changed files with 4 additions and 9 deletions.
11 changes: 3 additions & 8 deletions src/haplotyping/splitHaplotype.C
Original file line number Diff line number Diff line change
Expand Up @@ -413,14 +413,9 @@ hapData::initializeKmerTable(uint32 maxMemory) {
if (merylName[0]) {
merylFileReader *reader = new merylFileReader(merylName);

lookup = new merylExactLookup(reader, maxMemory, minFreq, UINT32_MAX);

if (lookup->configure() == false) {
exit(1);
}

lookup->load();

lookup = new merylExactLookup();
lookup->load(reader, maxMemory, true, false, minFreq, UINT32_MAX);

nKmers = lookup->nKmers();

delete reader;
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2 changes: 1 addition & 1 deletion src/utility
Submodule utility updated 46 files
+11 −0 src/Makefile
+26 −2 src/main.mk
+244 −0 src/parasail/cigar.c
+266 −0 src/parasail/cigar_template.c
+314 −0 src/parasail/config.h
+313 −0 src/parasail/cpuid.c
+31 −0 src/parasail/cpuid.h
+54 −0 src/parasail/internal_avx.h
+54 −0 src/parasail/internal_sse.h
+815 −0 src/parasail/memory.c
+70 −0 src/parasail/memory.h
+374 −0 src/parasail/memory_avx2.c
+374 −0 src/parasail/memory_sse.c
+74,918 −0 src/parasail/parasail.h
+206 −0 src/parasail/sg.c
+103 −0 src/parasail/sg_helper.h
+7,341 −0 src/parasail/sg_qb_de_dispatch.c
+7,346 −0 src/parasail/sg_qe_db_dispatch.c
+7,343 −0 src/parasail/sg_qx_dispatch.c
+185 −0 src/parasail/sg_trace.c
+411 −0 src/parasail/sg_trace_striped_avx2_256_16.c
+411 −0 src/parasail/sg_trace_striped_avx2_256_32.c
+398 −0 src/parasail/sg_trace_striped_sse2_128_16.c
+418 −0 src/parasail/sg_trace_striped_sse2_128_32.c
+393 −0 src/parasail/sg_trace_striped_sse41_128_16.c
+393 −0 src/parasail/sg_trace_striped_sse41_128_32.c
+119 −0 src/tests/alignTest-ksw2.C
+8 −0 src/tests/alignTest-ksw2.mk
+260 −0 src/tests/parasailTest.C
+10 −0 src/tests/parasailTest.mk
+23 −10 src/tests/systemTest.C
+8 −0 src/tests/systemTest.mk
+309 −0 src/utility/align-ksw2-driver.C
+130 −0 src/utility/align-ksw2-driver.H
+135 −0 src/utility/align-ksw2-extz.C
+305 −0 src/utility/align-ksw2-extz2-sse.C
+177 −0 src/utility/align-ksw2.H
+288 −0 src/utility/align-parasail-driver.C
+170 −0 src/utility/align-parasail-driver.H
+8 −0 src/utility/files.C
+142 −50 src/utility/kmers-exact.C
+100 −70 src/utility/kmers-lookup.H
+58 −24 src/utility/logging.C
+5 −0 src/utility/logging.H
+112 −2 src/utility/system.C
+5 −0 src/utility/system.H

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