Makefile | 19 8 + 11 - 0 !
src/filter/Makefile | 2 1 + 1 - 0 !
src/lumpy/Makefile | 34 16 + 18 - 0 !
src/utils/BamTools-Ancillary/Makefile | 5 2 + 3 - 0 !
src/utils/BlockedIntervals/Makefile | 7 3 + 4 - 0 !
src/utils/bedFile/Makefile | 5 2 + 3 - 0 !
src/utils/bedGraphFile/Makefile | 2 1 + 1 - 0 !
src/utils/genomeFile/Makefile | 2 1 + 1 - 0 !
src/utils/tabFile/Makefile | 5 2 + 3 - 0 !
9 files changed, 36 insertions(+), 45 deletions(-)

 use debian packaged libraries
 Please note: lumpy-sv contains a code copy of bedtools.  Unfortunately
 bedtools does not have a development library so its hard to replace this
 code copy here.

scripts/lumpyexpress | 18 9 + 9 - 0 !
1 file changed, 9 insertions(+), 9 deletions(-)

 adapt paths to debian locations

lumpy_tests/orig/bp_pesr.sh | 2 1 + 1 - 0 !
lumpy_tests/orig/bp_sr.sh | 2 1 + 1 - 0 !
scripts/bedpe_sort.py | 2 1 + 1 - 0 !
scripts/check_sorting.py | 2 1 + 1 - 0 !
scripts/cnvanator_to_bedpes.py | 2 1 + 1 - 0 !
scripts/extractSplitReads_BwaMem | 2 1 + 1 - 0 !
scripts/get_coverages.py | 2 1 + 1 - 0 !
scripts/get_exclude_regions.py | 2 1 + 1 - 0 !
scripts/l_merge.py | 2 1 + 1 - 0 !
scripts/l_sort.py | 2 1 + 1 - 0 !
scripts/pairend_distro.py | 2 1 + 1 - 0 !
scripts/prob_bedpe_to_bedgraph.py | 2 1 + 1 - 0 !
scripts/vcfToBedpe | 2 1 + 1 - 0 !
test/bp_pe.sh | 2 1 + 1 - 0 !
test/bp_pe_pl.sh | 2 1 + 1 - 0 !
test/bp_pesr.sh | 2 1 + 1 - 0 !
test/bp_pesr_pl.sh | 2 1 + 1 - 0 !
test/bp_sr.sh | 2 1 + 1 - 0 !
18 files changed, 18 insertions(+), 18 deletions(-)

 remove additional hash sign

Makefile | 4 2 + 2 - 0 !
src/filter/Makefile | 2 1 + 1 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 do not override dpkg provided c/cxxflags

Makefile | 1 1 + 0 - 0 !
src/filter/Makefile | 3 3 + 0 - 0 !
2 files changed, 4 insertions(+)

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