git-svn-id: http://biopieces.googlecode.com/svn/trunk@375 74ccb610-7750-0410-82ae...

diff --git a/bp_bin/00README b/bp_bin/00README
deleted file mode 100644 (file)
index 5991f9b..0000000
--- a/bp_bin/00README
+++ /dev/null
@@ -1,5 +0,0 @@
-This directory should only contain symlinks to Biopiece executables.
-
-
-
-Martin A. Hansen, June 2008

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
deleted file mode 120000 (symlink)
index f557754..0000000
--- a/bp_bin/add_ident
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/add_ident
\ No newline at end of file

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
deleted file mode 120000 (symlink)
index 0000796..0000000
--- a/bp_bin/align_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/align_seq
\ No newline at end of file

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
deleted file mode 120000 (symlink)
index 6f0d8ca..0000000
--- a/bp_bin/analyze_bed
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/analyze_bed
\ No newline at end of file

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
deleted file mode 120000 (symlink)
index ac17cf2..0000000
--- a/bp_bin/analyze_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/analyze_seq
\ No newline at end of file

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
deleted file mode 120000 (symlink)
index 3cb9f03..0000000
--- a/bp_bin/analyze_tags
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/analyze_tags
\ No newline at end of file

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
deleted file mode 120000 (symlink)
index c25d2e8..0000000
--- a/bp_bin/analyze_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/analyze_vals
\ No newline at end of file

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
deleted file mode 120000 (symlink)
index 2352792..0000000
--- a/bp_bin/assemble_tag_contigs
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/assemble_tag_contigs
\ No newline at end of file

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
deleted file mode 120000 (symlink)
index 27d57ad..0000000
--- a/bp_bin/blast_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/blast_seq
\ No newline at end of file

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
deleted file mode 120000 (symlink)
index eb77e30..0000000
--- a/bp_bin/blat_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/blat_seq
\ No newline at end of file

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
deleted file mode 120000 (symlink)
index 7105a3a..0000000
--- a/bp_bin/calc_bit_scores
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/calc_bit_scores
\ No newline at end of file

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
deleted file mode 120000 (symlink)
index b177a75..0000000
--- a/bp_bin/calc_fixedstep
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/calc_fixedstep
\ No newline at end of file

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
deleted file mode 120000 (symlink)
index c45e684..0000000
--- a/bp_bin/complement_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/complement_seq
\ No newline at end of file

diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq
deleted file mode 120000 (symlink)
index e67a447..0000000
--- a/bp_bin/complexity_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/complexity_seq
\ No newline at end of file

diff --git a/bp_bin/compute b/bp_bin/compute
deleted file mode 120000 (symlink)
index 073fa40..0000000
--- a/bp_bin/compute
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/compute
\ No newline at end of file

diff --git a/bp_bin/count_records b/bp_bin/count_records
deleted file mode 120000 (symlink)
index ba524a8..0000000
--- a/bp_bin/count_records
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/count_records
\ No newline at end of file

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
deleted file mode 120000 (symlink)
index 2574094..0000000
--- a/bp_bin/count_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/count_vals
\ No newline at end of file

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
deleted file mode 120000 (symlink)
index f7b9637..0000000
--- a/bp_bin/create_blast_db
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/create_blast_db
\ No newline at end of file

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
deleted file mode 120000 (symlink)
index 6590fad..0000000
--- a/bp_bin/create_vmatch_index
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/create_vmatch_index
\ No newline at end of file

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
deleted file mode 120000 (symlink)
index 17345c6..0000000
--- a/bp_bin/create_weight_matrix
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/create_weight_matrix
\ No newline at end of file

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
deleted file mode 120000 (symlink)
index bd5293f..0000000
--- a/bp_bin/extract_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/extract_seq
\ No newline at end of file

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
deleted file mode 120000 (symlink)
index 2703aa5..0000000
--- a/bp_bin/flip_tab
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/flip_tab
\ No newline at end of file

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
deleted file mode 120000 (symlink)
index c5f3728..0000000
--- a/bp_bin/fold_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/fold_seq
\ No newline at end of file

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
deleted file mode 120000 (symlink)
index c4b373b..0000000
--- a/bp_bin/format_genome
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/format_genome
\ No newline at end of file

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
deleted file mode 120000 (symlink)
index 65d4851..0000000
--- a/bp_bin/get_genome_align
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/get_genome_align
\ No newline at end of file

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
deleted file mode 120000 (symlink)
index e725c69..0000000
--- a/bp_bin/get_genome_phastcons
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/get_genome_phastcons
\ No newline at end of file

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
deleted file mode 120000 (symlink)
index 3f6c4cc..0000000
--- a/bp_bin/get_genome_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/get_genome_seq
\ No newline at end of file

diff --git a/bp_bin/grab b/bp_bin/grab
deleted file mode 120000 (symlink)
index 3319f75..0000000
--- a/bp_bin/grab
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/grab
\ No newline at end of file

diff --git a/bp_bin/head_records b/bp_bin/head_records
deleted file mode 120000 (symlink)
index db1b690..0000000
--- a/bp_bin/head_records
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/head_records
\ No newline at end of file

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
deleted file mode 120000 (symlink)
index 40c0b38..0000000
--- a/bp_bin/invert_align
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/invert_align
\ No newline at end of file

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
deleted file mode 120000 (symlink)
index b3a16a7..0000000
--- a/bp_bin/length_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/length_seq
\ No newline at end of file

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
deleted file mode 120000 (symlink)
index 4651536..0000000
--- a/bp_bin/length_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/length_vals
\ No newline at end of file

diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
deleted file mode 120000 (symlink)
index cb71814..0000000
--- a/bp_bin/list_biopieces
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/list_biopieces
\ No newline at end of file

diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
deleted file mode 120000 (symlink)
index 2ad4d09..0000000
--- a/bp_bin/list_genomes
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/list_genomes
\ No newline at end of file

diff --git a/bp_bin/lowercase_seq b/bp_bin/lowercase_seq
deleted file mode 120000 (symlink)
index 16158e9..0000000
--- a/bp_bin/lowercase_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_python/Cjung/lowercase_seq
\ No newline at end of file

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
deleted file mode 120000 (symlink)
index 2843de1..0000000
--- a/bp_bin/match_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/match_seq
\ No newline at end of file

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
deleted file mode 120000 (symlink)
index 0fd7620..0000000
--- a/bp_bin/max_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/max_vals
\ No newline at end of file

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
deleted file mode 120000 (symlink)
index 9d6fae5..0000000
--- a/bp_bin/mean_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/mean_vals
\ No newline at end of file

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
deleted file mode 120000 (symlink)
index dfcd775..0000000
--- a/bp_bin/median_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/median_vals
\ No newline at end of file

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
deleted file mode 120000 (symlink)
index 9da46f8..0000000
--- a/bp_bin/merge_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/merge_vals
\ No newline at end of file

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
deleted file mode 120000 (symlink)
index 089e58b..0000000
--- a/bp_bin/min_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/min_vals
\ No newline at end of file

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
deleted file mode 120000 (symlink)
index d2a9215..0000000
--- a/bp_bin/oligo_freq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/oligo_freq
\ No newline at end of file

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
deleted file mode 120000 (symlink)
index 45ff4a7..0000000
--- a/bp_bin/patscan_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/patscan_seq
\ No newline at end of file

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
deleted file mode 120000 (symlink)
index e88eb45..0000000
--- a/bp_bin/plot_chrdist
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/plot_chrdist
\ No newline at end of file

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
deleted file mode 120000 (symlink)
index 034da4e..0000000
--- a/bp_bin/plot_histogram
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/plot_histogram
\ No newline at end of file

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
deleted file mode 120000 (symlink)
index 99aeeba..0000000
--- a/bp_bin/plot_karyogram
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/plot_karyogram
\ No newline at end of file

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
deleted file mode 120000 (symlink)
index 66ddb3c..0000000
--- a/bp_bin/plot_lendist
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/plot_lendist
\ No newline at end of file

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
deleted file mode 120000 (symlink)
index 4c310f9..0000000
--- a/bp_bin/plot_matches
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/plot_matches
\ No newline at end of file

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
deleted file mode 120000 (symlink)
index 70757b2..0000000
--- a/bp_bin/plot_phastcons_profiles
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/plot_phastcons_profiles
\ No newline at end of file

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
deleted file mode 120000 (symlink)
index 236f33c..0000000
--- a/bp_bin/plot_seqlogo
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/plot_seqlogo
\ No newline at end of file

diff --git a/bp_bin/print_usage b/bp_bin/print_usage
deleted file mode 120000 (symlink)
index 8b05295..0000000
--- a/bp_bin/print_usage
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/print_usage
\ No newline at end of file

diff --git a/bp_bin/random_records b/bp_bin/random_records
deleted file mode 120000 (symlink)
index 2640774..0000000
--- a/bp_bin/random_records
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/random_records
\ No newline at end of file

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
deleted file mode 120000 (symlink)
index 9ddf362..0000000
--- a/bp_bin/read_2bit
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_2bit
\ No newline at end of file

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
deleted file mode 120000 (symlink)
index a0b3227..0000000
--- a/bp_bin/read_bed
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_bed
\ No newline at end of file

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
deleted file mode 120000 (symlink)
index 7041a55..0000000
--- a/bp_bin/read_blast_tab
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_blast_tab
\ No newline at end of file

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
deleted file mode 120000 (symlink)
index c7bf9e6..0000000
--- a/bp_bin/read_embl
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_embl
\ No newline at end of file

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
deleted file mode 120000 (symlink)
index 11935a9..0000000
--- a/bp_bin/read_fasta
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_fasta
\ No newline at end of file

diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
deleted file mode 120000 (symlink)
index 25baf02..0000000
--- a/bp_bin/read_fixedstep
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_fixedstep
\ No newline at end of file

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
deleted file mode 120000 (symlink)
index 879dad9..0000000
--- a/bp_bin/read_gff
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_gff
\ No newline at end of file

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
deleted file mode 120000 (symlink)
index 6f3bbd1..0000000
--- a/bp_bin/read_mysql
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_mysql
\ No newline at end of file

diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons
deleted file mode 120000 (symlink)
index ce7d6ff..0000000
--- a/bp_bin/read_phastcons
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_phastcons
\ No newline at end of file

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
deleted file mode 120000 (symlink)
index 9ea2e70..0000000
--- a/bp_bin/read_psl
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_psl
\ No newline at end of file

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
deleted file mode 120000 (symlink)
index 339b425..0000000
--- a/bp_bin/read_soft
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_soft
\ No newline at end of file

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
deleted file mode 120000 (symlink)
index a38e5d8..0000000
--- a/bp_bin/read_solexa
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_solexa
\ No newline at end of file

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
deleted file mode 120000 (symlink)
index cf25cc4..0000000
--- a/bp_bin/read_solid
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_solid
\ No newline at end of file

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
deleted file mode 120000 (symlink)
index e203eb4..0000000
--- a/bp_bin/read_stockholm
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_stockholm
\ No newline at end of file

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
deleted file mode 120000 (symlink)
index 05c6209..0000000
--- a/bp_bin/read_tab
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_tab
\ No newline at end of file

diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
deleted file mode 120000 (symlink)
index 5247bd7..0000000
--- a/bp_bin/read_ucsc_config
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/read_ucsc_config
\ No newline at end of file

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
deleted file mode 120000 (symlink)
index 639285c..0000000
--- a/bp_bin/remove_adaptor
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/remove_adaptor
\ No newline at end of file

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
deleted file mode 120000 (symlink)
index 52c84d9..0000000
--- a/bp_bin/remove_indels
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/remove_indels
\ No newline at end of file

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
deleted file mode 120000 (symlink)
index afb4076..0000000
--- a/bp_bin/remove_keys
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/remove_keys
\ No newline at end of file

diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
deleted file mode 120000 (symlink)
index 39a2428..0000000
--- a/bp_bin/remove_mysql_tables
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/remove_mysql_tables
\ No newline at end of file

diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
deleted file mode 120000 (symlink)
index fa1f7ca..0000000
--- a/bp_bin/remove_ucsc_tracks
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/remove_ucsc_tracks
\ No newline at end of file

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
deleted file mode 120000 (symlink)
index 78541e1..0000000
--- a/bp_bin/rename_keys
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/rename_keys
\ No newline at end of file

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
deleted file mode 120000 (symlink)
index 2ae4226..0000000
--- a/bp_bin/reverse_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/reverse_seq
\ No newline at end of file

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
deleted file mode 120000 (symlink)
index e9f42f1..0000000
--- a/bp_bin/shuffle_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/shuffle_seq
\ No newline at end of file

diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
deleted file mode 120000 (symlink)
index 7920fbc..0000000
--- a/bp_bin/soap_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/soap_seq
\ No newline at end of file

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
deleted file mode 120000 (symlink)
index 6ff6dd3..0000000
--- a/bp_bin/sort_records
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/sort_records
\ No newline at end of file

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
deleted file mode 120000 (symlink)
index 89c5725..0000000
--- a/bp_bin/split_bed
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/split_bed
\ No newline at end of file

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
deleted file mode 120000 (symlink)
index a428a1e..0000000
--- a/bp_bin/split_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/split_seq
\ No newline at end of file

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
deleted file mode 120000 (symlink)
index 4193a49..0000000
--- a/bp_bin/sum_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/sum_vals
\ No newline at end of file

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
deleted file mode 120000 (symlink)
index f026ddd..0000000
--- a/bp_bin/tile_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/tile_seq
\ No newline at end of file

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
deleted file mode 120000 (symlink)
index 3e8ae5e..0000000
--- a/bp_bin/translate_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/translate_seq
\ No newline at end of file

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
deleted file mode 120000 (symlink)
index ce6ea54..0000000
--- a/bp_bin/transliterate_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/transliterate_seq
\ No newline at end of file

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
deleted file mode 120000 (symlink)
index bf8d8e2..0000000
--- a/bp_bin/transliterate_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/transliterate_vals
\ No newline at end of file

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
deleted file mode 120000 (symlink)
index fb3bafc..0000000
--- a/bp_bin/uniq_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/uniq_vals
\ No newline at end of file

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
deleted file mode 120000 (symlink)
index e97a1eb..0000000
--- a/bp_bin/upload_to_ucsc
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/upload_to_ucsc
\ No newline at end of file

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
deleted file mode 120000 (symlink)
index d149da2..0000000
--- a/bp_bin/uppercase_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/uppercase_seq
\ No newline at end of file

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
deleted file mode 120000 (symlink)
index f98275c..0000000
--- a/bp_bin/vmatch_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/vmatch_seq
\ No newline at end of file

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
deleted file mode 120000 (symlink)
index 3b58b31..0000000
--- a/bp_bin/write_2bit
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_2bit
\ No newline at end of file

diff --git a/bp_bin/write_align b/bp_bin/write_align
deleted file mode 120000 (symlink)
index 15fd96a..0000000
--- a/bp_bin/write_align
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_align
\ No newline at end of file

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
deleted file mode 120000 (symlink)
index 38a4411..0000000
--- a/bp_bin/write_bed
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_bed
\ No newline at end of file

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
deleted file mode 120000 (symlink)
index e84bd5c..0000000
--- a/bp_bin/write_blast
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_blast
\ No newline at end of file

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
deleted file mode 120000 (symlink)
index d7afcfb..0000000
--- a/bp_bin/write_fasta
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_fasta
\ No newline at end of file

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
deleted file mode 120000 (symlink)
index 67f50bb..0000000
--- a/bp_bin/write_fixedstep
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_fixedstep
\ No newline at end of file

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
deleted file mode 120000 (symlink)
index edf73ff..0000000
--- a/bp_bin/write_psl
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_psl
\ No newline at end of file

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
deleted file mode 120000 (symlink)
index 48c24a4..0000000
--- a/bp_bin/write_solid
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_solid
\ No newline at end of file

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
deleted file mode 120000 (symlink)
index 1a45ade..0000000
--- a/bp_bin/write_tab
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_tab
\ No newline at end of file

diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
deleted file mode 120000 (symlink)
index d25e997..0000000
--- a/bp_bin/write_ucsc_config
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/write_ucsc_config
\ No newline at end of file