apply_scoring_matrix_in_place4.py@
bad_junctions.txt@
calculate_baseline_coverage_probes.pl@
chr_order.sorted.dbsnp_131_hg19.rod@
Chr_snps_size.txt@
collapse_exon_file.pl@
count_mips_design_character.pl@
dbsnp_130_hg18.rod@
design_all_mips_joe1.pl@
design_all_mips_joe2.pl@
design_all_mips.pl@
fasta_list_hg18@
fasta_list_hg19@
generate_70mers2.py@
generate_ucsc_track_colors.py@
generate_ucsc_track.py@
genome_compare@
get_design_region.pl@
get_region_exons.pl@
hg18@
hg19@
makeBedFromList.py@
makeRunMipDesignShellScript2.py@
MIP_README.txt*
pick_mips3.pl@
pick_mips4_double_up_on_small_BJO.pl@
pick_mips4_double_up_on_small.pl@
redesign_mips_with_snps.pl@
scoring_matrix_v4.txt.csv@
snp132.txt@
uniformity_functions.py@

genome_compare_distrib:
binaries/
build.sh*
genome_compare.cpp*

testfiles:
1st-TESTFILES_README.txt*
Chr_snps_size.txt*
KATNB1_16_24.apply_scoring_matrix_in_place4.se*
KATNB1_16_24.apply_scoring_matrix_in_place4.so*
KATNB1_16_24.copy_counts.se*
KATNB1_16_24.copy_counts.so*
KATNB1_16_24.design_all_mips_joe2.se*
KATNB1_16_24.design_all_mips_joe2.so*
KATNB1_17_23.apply_scoring_matrix_in_place4.se*
KATNB1_17_23.apply_scoring_matrix_in_place4.so*
KATNB1_17_23.copy_counts.se*
KATNB1_17_23.copy_counts.so*
KATNB1_17_23.design_all_mips_joe2.se*
KATNB1_17_23.design_all_mips_joe2.so*
KATNB1_18_22.apply_scoring_matrix_in_place4.se*
KATNB1_18_22.apply_scoring_matrix_in_place4.so*
KATNB1_18_22.copy_counts.se*
KATNB1_18_22.copy_counts.so*
KATNB1_18_22.design_all_mips_joe2.se*
KATNB1_18_22.design_all_mips_joe2.so*
KATNB1_19_21.apply_scoring_matrix_in_place4.se*
KATNB1_19_21.apply_scoring_matrix_in_place4.so*
KATNB1_19_21.copy_counts.se*
KATNB1_19_21.copy_counts.so*
KATNB1_19_21.design_all_mips_joe2.se*
KATNB1_19_21.design_all_mips_joe2.so*
KATNB1_20_20.apply_scoring_matrix_in_place4.se*
KATNB1_20_20.apply_scoring_matrix_in_place4.so*
KATNB1_20_20.copy_counts.se*
KATNB1_20_20.copy_counts.so*
KATNB1_20_20.design_all_mips_joe2.se*
KATNB1_20_20.design_all_mips_joe2.so*
KATNB1_70mers.txt*
KATNB1.pick_mips4.se*
KATNB1.pick_mips4.so*
KATNB1.sh*
KATNB1_ucsc.bed*
testcoordinates.bed*
testcoordinates.bed.ext16.lig24.scan112.all_mips*
testcoordinates.bed.ext16.lig24.scan112.all_mips.copy_counts*
testcoordinates.bed.ext16.lig24.scan112.all_mips.copy_counts.ranked*
testcoordinates.bed.ext17.lig23.scan112.all_mips*
testcoordinates.bed.ext17.lig23.scan112.all_mips.copy_counts*
testcoordinates.bed.ext17.lig23.scan112.all_mips.copy_counts.ranked*
testcoordinates.bed.ext18.lig22.scan112.all_mips*
testcoordinates.bed.ext18.lig22.scan112.all_mips.copy_counts*
testcoordinates.bed.ext18.lig22.scan112.all_mips.copy_counts.ranked*
testcoordinates.bed.ext19.lig21.scan112.all_mips*
testcoordinates.bed.ext19.lig21.scan112.all_mips.copy_counts*
testcoordinates.bed.ext19.lig21.scan112.all_mips.copy_counts.ranked*
testcoordinates.bed.ext20.lig20.scan112.all_mips*
testcoordinates.bed.ext20.lig20.scan112.all_mips.copy_counts*
testcoordinates.bed.ext20.lig20.scan112.all_mips.copy_counts.ranked*
testcoordinates.bed.picked_mip_probe_arms.testcoordinates.bed.scan112.all_mips.copy_counts.ranked.ranked_list.txt*
testcoordinates.bed.picked_mip_probe_arms.testcoordinates.bed.scan112.all_mips.copy_counts.ranked.ranked_list.txt.fixed_snps*
testcoordinates.bed.scan112.all_mips.copy_counts.ranked.ranked_list.txt*