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maps seed contigs back and retain only those in some connected compon…
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…ents as seed hits for subasm
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alex bishara committed Aug 13, 2017
1 parent 709471f commit 74f8d87
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Showing 11 changed files with 287 additions and 168 deletions.
120 changes: 60 additions & 60 deletions BUILD
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Expand Up @@ -44,240 +44,240 @@ cc_binary(
)

cc_binary(
name = "fq2fa",
srcs = ["src/release/fq2fa.cpp"],
name = "idba_hybrid",
srcs = ["src/release/idba_hybrid.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "idba",
srcs = ["src/release/idba.cpp"],
name = "idba_subasm",
srcs = ["src/release/idba_subasm.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "idba_hybrid",
srcs = ["src/release/idba_hybrid.cpp"],
name = "sim_reads_tran",
srcs = ["src/release/sim_reads_tran.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "idba_tran",
srcs = ["src/release/idba_tran.cpp"],
name = "idba",
srcs = ["src/release/idba.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "idba_subasm",
srcs = ["src/release/idba_subasm.cpp"],
name = "parallel_blat",
srcs = ["src/release/parallel_blat.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "idba_ud",
srcs = ["src/release/idba_ud.cpp"],
name = "idba_tran",
srcs = ["src/release/idba_tran.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "parallel_blat",
srcs = ["src/release/parallel_blat.cpp"],
name = "split_scaffold",
srcs = ["src/release/split_scaffold.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "raw_n50",
srcs = ["src/release/raw_n50.cpp"],
name = "sim_reads",
srcs = ["src/release/sim_reads.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "sim_reads",
srcs = ["src/release/sim_reads.cpp"],
name = "fq2fa",
srcs = ["src/release/fq2fa.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "sim_reads_tran",
srcs = ["src/release/sim_reads_tran.cpp"],
name = "validate_contigs_blat",
srcs = ["src/release/validate_contigs_blat.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "split_scaffold",
srcs = ["src/release/split_scaffold.cpp"],
name = "raw_n50",
srcs = ["src/release/raw_n50.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "validate_contigs_blat",
srcs = ["src/release/validate_contigs_blat.cpp"],
name = "idba_ud",
srcs = ["src/release/idba_ud.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "fa2fq",
srcs = ["src/tools/fa2fq.cpp"],
name = "idba_tran_test",
srcs = ["src/tools/idba_tran_test.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "filter_blat",
srcs = ["src/tools/filter_blat.cpp"],
name = "validate_component",
srcs = ["src/tools/validate_component.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "filter_contigs",
srcs = ["src/tools/filter_contigs.cpp"],
name = "print_graph",
srcs = ["src/tools/print_graph.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "idba_tran_test",
srcs = ["src/tools/idba_tran_test.cpp"],
name = "scaffold",
srcs = ["src/tools/scaffold.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "parallel_rna_blat",
srcs = ["src/tools/parallel_rna_blat.cpp"],
name = "split_fq",
srcs = ["src/tools/split_fq.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "print_graph",
srcs = ["src/tools/print_graph.cpp"],
name = "test",
srcs = ["src/tools/test.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "sample_reads",
srcs = ["src/tools/sample_reads.cpp"],
name = "filter_blat",
srcs = ["src/tools/filter_blat.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "scaffold",
srcs = ["src/tools/scaffold.cpp"],
name = "validate_reads_blat",
srcs = ["src/tools/validate_reads_blat.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "shuffle_reads",
srcs = ["src/tools/shuffle_reads.cpp"],
name = "sample_reads",
srcs = ["src/tools/sample_reads.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "sort_psl",
srcs = ["src/tools/sort_psl.cpp"],
name = "fa2fq",
srcs = ["src/tools/fa2fq.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "sort_reads",
srcs = ["src/tools/sort_reads.cpp"],
name = "validate_rna",
srcs = ["src/tools/validate_rna.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "split_fa",
srcs = ["src/tools/split_fa.cpp"],
name = "sort_psl",
srcs = ["src/tools/sort_psl.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "split_fq",
srcs = ["src/tools/split_fq.cpp"],
name = "validate_contigs_mummer",
srcs = ["src/tools/validate_contigs_mummer.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "test",
srcs = ["src/tools/test.cpp"],
name = "parallel_rna_blat",
srcs = ["src/tools/parallel_rna_blat.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "validate_component",
srcs = ["src/tools/validate_component.cpp"],
name = "filter_contigs",
srcs = ["src/tools/filter_contigs.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "validate_contigs_mummer",
srcs = ["src/tools/validate_contigs_mummer.cpp"],
name = "split_fa",
srcs = ["src/tools/split_fa.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "validate_reads_blat",
srcs = ["src/tools/validate_reads_blat.cpp"],
name = "sort_reads",
srcs = ["src/tools/sort_reads.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
)

cc_binary(
name = "validate_rna",
srcs = ["src/tools/validate_rna.cpp"],
name = "shuffle_reads",
srcs = ["src/tools/shuffle_reads.cpp"],
copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
linkopts = ["-pthread", "-fopenmp", "-lm"],
deps = [":assembly"],
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