From b817a3ff6e6cadd0598baec0772050e167e9b29d Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 13 May 2009 15:20:09 +0000 Subject: [PATCH] git-svn-id: http://biopieces.googlecode.com/svn/trunk@375 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/00README | 5 ----- bp_bin/add_ident | 1 - bp_bin/align_seq | 1 - bp_bin/analyze_bed | 1 - bp_bin/analyze_seq | 1 - bp_bin/analyze_tags | 1 - bp_bin/analyze_vals | 1 - bp_bin/assemble_tag_contigs | 1 - bp_bin/blast_seq | 1 - bp_bin/blat_seq | 1 - bp_bin/calc_bit_scores | 1 - bp_bin/calc_fixedstep | 1 - bp_bin/complement_seq | 1 - bp_bin/complexity_seq | 1 - bp_bin/compute | 1 - bp_bin/count_records | 1 - bp_bin/count_vals | 1 - bp_bin/create_blast_db | 1 - bp_bin/create_vmatch_index | 1 - bp_bin/create_weight_matrix | 1 - bp_bin/extract_seq | 1 - bp_bin/flip_tab | 1 - bp_bin/fold_seq | 1 - bp_bin/format_genome | 1 - bp_bin/get_genome_align | 1 - bp_bin/get_genome_phastcons | 1 - bp_bin/get_genome_seq | 1 - bp_bin/grab | 1 - bp_bin/head_records | 1 - bp_bin/invert_align | 1 - bp_bin/length_seq | 1 - bp_bin/length_vals | 1 - bp_bin/list_biopieces | 1 - bp_bin/list_genomes | 1 - bp_bin/lowercase_seq | 1 - bp_bin/match_seq | 1 - bp_bin/max_vals | 1 - bp_bin/mean_vals | 1 - bp_bin/median_vals | 1 - bp_bin/merge_vals | 1 - bp_bin/min_vals | 1 - bp_bin/oligo_freq | 1 - bp_bin/patscan_seq | 1 - bp_bin/plot_chrdist | 1 - bp_bin/plot_histogram | 1 - bp_bin/plot_karyogram | 1 - bp_bin/plot_lendist | 1 - bp_bin/plot_matches | 1 - bp_bin/plot_phastcons_profiles | 1 - bp_bin/plot_seqlogo | 1 - bp_bin/print_usage | 1 - bp_bin/random_records | 1 - bp_bin/read_2bit | 1 - bp_bin/read_bed | 1 - bp_bin/read_blast_tab | 1 - bp_bin/read_embl | 1 - bp_bin/read_fasta | 1 - bp_bin/read_fixedstep | 1 - bp_bin/read_gff | 1 - bp_bin/read_mysql | 1 - bp_bin/read_phastcons | 1 - bp_bin/read_psl | 1 - bp_bin/read_soft | 1 - bp_bin/read_solexa | 1 - bp_bin/read_solid | 1 - bp_bin/read_stockholm | 1 - bp_bin/read_tab | 1 - bp_bin/read_ucsc_config | 1 - bp_bin/remove_adaptor | 1 - bp_bin/remove_indels | 1 - bp_bin/remove_keys | 1 - bp_bin/remove_mysql_tables | 1 - bp_bin/remove_ucsc_tracks | 1 - bp_bin/rename_keys | 1 - bp_bin/reverse_seq | 1 - bp_bin/shuffle_seq | 1 - bp_bin/soap_seq | 1 - bp_bin/sort_records | 1 - bp_bin/split_bed | 1 - bp_bin/split_seq | 1 - bp_bin/sum_vals | 1 - bp_bin/tile_seq | 1 - bp_bin/translate_seq | 1 - bp_bin/transliterate_seq | 1 - bp_bin/transliterate_vals | 1 - bp_bin/uniq_vals | 1 - bp_bin/upload_to_ucsc | 1 - bp_bin/uppercase_seq | 1 - bp_bin/vmatch_seq | 1 - bp_bin/write_2bit | 1 - bp_bin/write_align | 1 - bp_bin/write_bed | 1 - bp_bin/write_blast | 1 - bp_bin/write_fasta | 1 - bp_bin/write_fixedstep | 1 - bp_bin/write_psl | 1 - bp_bin/write_solid | 1 - bp_bin/write_tab | 1 - bp_bin/write_ucsc_config | 1 - 99 files changed, 103 deletions(-) delete mode 100644 bp_bin/00README delete mode 120000 bp_bin/add_ident delete mode 120000 bp_bin/align_seq delete mode 120000 bp_bin/analyze_bed delete mode 120000 bp_bin/analyze_seq delete mode 120000 bp_bin/analyze_tags delete mode 120000 bp_bin/analyze_vals delete mode 120000 bp_bin/assemble_tag_contigs delete mode 120000 bp_bin/blast_seq delete mode 120000 bp_bin/blat_seq delete mode 120000 bp_bin/calc_bit_scores delete mode 120000 bp_bin/calc_fixedstep delete mode 120000 bp_bin/complement_seq delete mode 120000 bp_bin/complexity_seq delete mode 120000 bp_bin/compute delete mode 120000 bp_bin/count_records delete mode 120000 bp_bin/count_vals delete mode 120000 bp_bin/create_blast_db delete mode 120000 bp_bin/create_vmatch_index delete mode 120000 bp_bin/create_weight_matrix delete mode 120000 bp_bin/extract_seq delete mode 120000 bp_bin/flip_tab delete mode 120000 bp_bin/fold_seq delete mode 120000 bp_bin/format_genome delete mode 120000 bp_bin/get_genome_align delete mode 120000 bp_bin/get_genome_phastcons delete mode 120000 bp_bin/get_genome_seq delete mode 120000 bp_bin/grab delete mode 120000 bp_bin/head_records delete mode 120000 bp_bin/invert_align delete mode 120000 bp_bin/length_seq delete mode 120000 bp_bin/length_vals delete mode 120000 bp_bin/list_biopieces delete mode 120000 bp_bin/list_genomes delete mode 120000 bp_bin/lowercase_seq delete mode 120000 bp_bin/match_seq delete mode 120000 bp_bin/max_vals delete mode 120000 bp_bin/mean_vals delete mode 120000 bp_bin/median_vals delete mode 120000 bp_bin/merge_vals delete mode 120000 bp_bin/min_vals delete mode 120000 bp_bin/oligo_freq delete mode 120000 bp_bin/patscan_seq delete mode 120000 bp_bin/plot_chrdist delete mode 120000 bp_bin/plot_histogram delete mode 120000 bp_bin/plot_karyogram delete mode 120000 bp_bin/plot_lendist delete mode 120000 bp_bin/plot_matches delete mode 120000 bp_bin/plot_phastcons_profiles delete mode 120000 bp_bin/plot_seqlogo delete mode 120000 bp_bin/print_usage delete mode 120000 bp_bin/random_records delete mode 120000 bp_bin/read_2bit delete mode 120000 bp_bin/read_bed delete mode 120000 bp_bin/read_blast_tab delete mode 120000 bp_bin/read_embl delete mode 120000 bp_bin/read_fasta delete mode 120000 bp_bin/read_fixedstep delete mode 120000 bp_bin/read_gff delete mode 120000 bp_bin/read_mysql delete mode 120000 bp_bin/read_phastcons delete mode 120000 bp_bin/read_psl delete mode 120000 bp_bin/read_soft delete mode 120000 bp_bin/read_solexa delete mode 120000 bp_bin/read_solid delete mode 120000 bp_bin/read_stockholm delete mode 120000 bp_bin/read_tab delete mode 120000 bp_bin/read_ucsc_config delete mode 120000 bp_bin/remove_adaptor delete mode 120000 bp_bin/remove_indels delete mode 120000 bp_bin/remove_keys delete mode 120000 bp_bin/remove_mysql_tables delete mode 120000 bp_bin/remove_ucsc_tracks delete mode 120000 bp_bin/rename_keys delete mode 120000 bp_bin/reverse_seq delete mode 120000 bp_bin/shuffle_seq delete mode 120000 bp_bin/soap_seq delete mode 120000 bp_bin/sort_records delete mode 120000 bp_bin/split_bed delete mode 120000 bp_bin/split_seq delete mode 120000 bp_bin/sum_vals delete mode 120000 bp_bin/tile_seq delete mode 120000 bp_bin/translate_seq delete mode 120000 bp_bin/transliterate_seq delete mode 120000 bp_bin/transliterate_vals delete mode 120000 bp_bin/uniq_vals delete mode 120000 bp_bin/upload_to_ucsc delete mode 120000 bp_bin/uppercase_seq delete mode 120000 bp_bin/vmatch_seq delete mode 120000 bp_bin/write_2bit delete mode 120000 bp_bin/write_align delete mode 120000 bp_bin/write_bed delete mode 120000 bp_bin/write_blast delete mode 120000 bp_bin/write_fasta delete mode 120000 bp_bin/write_fixedstep delete mode 120000 bp_bin/write_psl delete mode 120000 bp_bin/write_solid delete mode 120000 bp_bin/write_tab delete mode 120000 bp_bin/write_ucsc_config diff --git a/bp_bin/00README b/bp_bin/00README deleted file mode 100644 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 -- 2.39.2