git.donarmstrong.com Git - biopieces.git/tree

drwxr-xr-x		..
-rw-r--r--	88	00README	blob \| history \| raw
-rwxr-xr-x	3552	BGB_delete_track	blob \| history \| raw
-rwxr-xr-x	4495	BGB_intersect	blob \| history \| raw
-rwxr-xr-x	3877	BGB_list	blob \| history \| raw
-rwxr-xr-x	3774	BGB_read_track	blob \| history \| raw
-rwxr-xr-x	6593	BGB_upload	blob \| history \| raw
-rwxr-xr-x	2531	add_ident	blob \| history \| raw
-rwxr-xr-x	1897	align_pair_seq	blob \| history \| raw
-rwxr-xr-x	2683	align_seq	blob \| history \| raw
-rwxr-xr-x	3296	analyze_assembly	blob \| history \| raw
-rwxr-xr-x	2021	analyze_bed	blob \| history \| raw
-rwxr-xr-x	2220	analyze_gc	blob \| history \| raw
-rwxr-xr-x	1977	analyze_seq	blob \| history \| raw
-rwxr-xr-x	3860	analyze_snp	blob \| history \| raw
-rwxr-xr-x	2794	analyze_tags	blob \| history \| raw
-rwxr-xr-x	5441	analyze_vals	blob \| history \| raw
-rwxr-xr-x	5854	assemble_contigs	blob \| history \| raw
-rwxr-xr-x	3584	assemble_pairs	blob \| history \| raw
-rwxr-xr-x	3869	assemble_seq_idba	blob \| history \| raw
-rwxr-xr-x	5098	assemble_seq_ray	blob \| history \| raw
-rwxr-xr-x	5898	assemble_seq_velvet	blob \| history \| raw
-rwxr-xr-x	4041	assemble_tag_contigs	blob \| history \| raw
-rwxr-xr-x	1987	bin_vals	blob \| history \| raw
-rwxr-xr-x	2200	bioscript	blob \| history \| raw
-rwxr-xr-x	5761	biostat	blob \| history \| raw
-rwxr-xr-x	9482	blast_seq	blob \| history \| raw
-rwxr-xr-x	6312	blast_seq_pair	blob \| history \| raw
-rwxr-xr-x	5783	blat_seq	blob \| history \| raw
-rwxr-xr-x	3698	bowtie2_seq	blob \| history \| raw
-rwxr-xr-x	6717	bowtie_seq	blob \| history \| raw
-rwxr-xr-x	3815	bwa_seq	blob \| history \| raw
-rwxr-xr-x	2214	calc_N50	blob \| history \| raw
-rwxr-xr-x	2809	calc_bit_scores	blob \| history \| raw
lrwxrwxrwx	33	calc_density -> ../code_python/Cjung/calc_density	blob \| history \| raw
-rwxr-xr-x	3548	calc_fixedstep	blob \| history \| raw
-rwxr-xr-x	6179	classify_taxonomy	blob \| history \| raw
-rwxr-xr-x	2091	clip_adaptor	blob \| history \| raw
-rwxr-xr-x	2028	clip_seq	blob \| history \| raw
-rwxr-xr-x	2281	complement_seq	blob \| history \| raw
-rwxr-xr-x	3165	compute	blob \| history \| raw
-rwxr-xr-x	2640	count_records	blob \| history \| raw
-rwxr-xr-x	3549	count_vals	blob \| history \| raw
-rwxr-xr-x	3419	create_blast_index	blob \| history \| raw
-rwxr-xr-x	2561	create_bowtie2_index	blob \| history \| raw
-rwxr-xr-x	3067	create_bowtie_index	blob \| history \| raw
-rwxr-xr-x	3049	create_bwa_index	blob \| history \| raw
-rwxr-xr-x	3172	create_fixedstep_index	blob \| history \| raw
-rwxr-xr-x	2996	create_seq_index	blob \| history \| raw
-rwxr-xr-x	3187	create_vmatch_index	blob \| history \| raw
-rwxr-xr-x	2899	create_weight_matrix	blob \| history \| raw
-rwxr-xr-x	4331	denoise_seq	blob \| history \| raw
-rwxr-xr-x	2329	digest_seq	blob \| history \| raw
-rwxr-xr-x	1824	duplicate_record	blob \| history \| raw
-rwxr-xr-x	2952	embl_index	blob \| history \| raw
-rwxr-xr-x	4252	extract_seq	blob \| history \| raw
-rwxr-xr-x	3109	find_SNPs	blob \| history \| raw
-rwxr-xr-x	6286	find_adaptor	blob \| history \| raw
-rwxr-xr-x	9995	find_barcodes	blob \| history \| raw
-rwxr-xr-x	3353	find_gaps	blob \| history \| raw
-rwxr-xr-x	2313	find_genes	blob \| history \| raw
-rwxr-xr-x	2906	find_homopolymers	blob \| history \| raw
-rwxr-xr-x	2797	find_orfs	blob \| history \| raw
-rwxr-xr-x	2407	find_orphans	blob \| history \| raw
-rwxr-xr-x	2362	find_pairs	blob \| history \| raw
-rwxr-xr-x	3313	findsim_seq	blob \| history \| raw
-rwxr-xr-x	2399	flip_tab	blob \| history \| raw
-rwxr-xr-x	2477	fold_seq	blob \| history \| raw
-rwxr-xr-x	5509	format_genome	blob \| history \| raw
-rwxr-xr-x	4828	get_embl_entry	blob \| history \| raw
-rwxr-xr-x	5742	get_fixedstep	blob \| history \| raw
-rwxr-xr-x	6184	get_genome_align	blob \| history \| raw
-rwxr-xr-x	5204	get_genome_phastcons	blob \| history \| raw
-rwxr-xr-x	8139	get_genome_seq	blob \| history \| raw
-rwxr-xr-x	5569	get_seq	blob \| history \| raw
-rwxr-xr-x	9756	grab	blob \| history \| raw
-rwxr-xr-x	2148	head_records	blob \| history \| raw
-rwxr-xr-x	5569	hmmer_seq	blob \| history \| raw
-rwxr-xr-x	3386	indel_seq	blob \| history \| raw
-rwxr-xr-x	1862	index_vals	blob \| history \| raw
-rwxr-xr-x	3955	intersect_records	blob \| history \| raw
-rwxr-xr-x	2542	invert_align	blob \| history \| raw
-rwxr-xr-x	2061	join_seq	blob \| history \| raw
-rwxr-xr-x	2174	kmer_freq	blob \| history \| raw
-rwxr-xr-x	1621	length_seq	blob \| history \| raw
-rwxr-xr-x	2254	length_vals	blob \| history \| raw
-rwxr-xr-x	2006	list_biopieces	blob \| history \| raw
-rwxr-xr-x	2425	list_genomes	blob \| history \| raw
-rwxr-xr-x	2217	list_mysql_databases	blob \| history \| raw
lrwxrwxrwx	34	lowercase_seq -> ../code_python/Cjung/lowercase_seq	blob \| history \| raw
-rwxr-xr-x	2032	mask_seq	blob \| history \| raw
-rwxr-xr-x	2858	match_seq	blob \| history \| raw
-rwxr-xr-x	4273	mate_pair_dist	blob \| history \| raw
-rwxr-xr-x	3740	max_vals	blob \| history \| raw
-rwxr-xr-x	3731	mean_scores	blob \| history \| raw
-rwxr-xr-x	3753	mean_vals	blob \| history \| raw
-rwxr-xr-x	3682	median_vals	blob \| history \| raw
-rwxr-xr-x	2704	merge_pair_seq	blob \| history \| raw
-rwxr-xr-x	5981	merge_records	blob \| history \| raw
-rwxr-xr-x	2630	merge_vals	blob \| history \| raw
-rwxr-xr-x	3739	min_vals	blob \| history \| raw
-rwxr-xr-x	3274	mutate_seq	blob \| history \| raw
-rwxr-xr-x	2786	oligo_freq	blob \| history \| raw
-rwxr-xr-x	2633	order_pairs	blob \| history \| raw
-rwxr-xr-x	7331	patscan_seq	blob \| history \| raw
-rwxr-xr-x	6252	pcr_seq	blob \| history \| raw
-rwxr-xr-x	4450	plot_chrdist	blob \| history \| raw
-rwxr-xr-x	3556	plot_distribution	blob \| history \| raw
-rwxr-xr-x	3964	plot_histogram	blob \| history \| raw
-rwxr-xr-x	3118	plot_karyogram	blob \| history \| raw
-rwxr-xr-x	3779	plot_lendist	blob \| history \| raw
-rwxr-xr-x	4585	plot_lines	blob \| history \| raw
-rwxr-xr-x	7078	plot_matches	blob \| history \| raw
-rwxr-xr-x	5634	plot_nucleotide_distribution	blob \| history \| raw
-rwxr-xr-x	5279	plot_phastcons_profiles	blob \| history \| raw
-rwxr-xr-x	4082	plot_scores	blob \| history \| raw
-rwxr-xr-x	2571	plot_seqlogo	blob \| history \| raw
-rwxr-xr-x	4709	plot_stacked_histogram	blob \| history \| raw
-rwxr-xr-x	2263	print_wiki	blob \| history \| raw
-rwxr-xr-x	2077	progress_meter	blob \| history \| raw
-rwxr-xr-x	2994	random_records	blob \| history \| raw
-rwxr-xr-x	3140	read_2bit	blob \| history \| raw
-rwxr-xr-x	5082	read_454	blob \| history \| raw
-rwxr-xr-x	2786	read_ace	blob \| history \| raw
-rwxr-xr-x	3078	read_bed	blob \| history \| raw
-rwxr-xr-x	3757	read_blast_tab	blob \| history \| raw
-rwxr-xr-x	2955	read_embl	blob \| history \| raw
-rwxr-xr-x	2273	read_fasta	blob \| history \| raw
-rwxr-xr-x	4550	read_fastq	blob \| history \| raw
-rwxr-xr-x	2729	read_fixedstep	blob \| history \| raw
-rwxr-xr-x	2955	read_genbank	blob \| history \| raw
-rwxr-xr-x	2703	read_gff	blob \| history \| raw
-rwxr-xr-x	2712	read_kiss	blob \| history \| raw
-rwxr-xr-x	2967	read_mysql	blob \| history \| raw
-rwxr-xr-x	2761	read_psl	blob \| history \| raw
-rwxr-xr-x	2190	read_sam	blob \| history \| raw
-rwxr-xr-x	2517	read_sff	blob \| history \| raw
-rwxr-xr-x	4131	read_soft	blob \| history \| raw
-rwxr-xr-x	3514	read_solid	blob \| history \| raw
-rwxr-xr-x	3297	read_stockholm	blob \| history \| raw
-rwxr-xr-x	4140	read_tab	blob \| history \| raw
-rwxr-xr-x	2693	read_ucsc_config	blob \| history \| raw
-rwxr-xr-x	4000	remove_adaptor	blob \| history \| raw
-rwxr-xr-x	2374	remove_indel_columns	blob \| history \| raw
-rwxr-xr-x	2033	remove_indels	blob \| history \| raw
-rwxr-xr-x	2551	remove_keys	blob \| history \| raw
-rwxr-xr-x	4012	remove_mysql_tables	blob \| history \| raw
-rwxr-xr-x	3279	remove_primers	blob \| history \| raw
-rwxr-xr-x	4974	remove_ucsc_tracks	blob \| history \| raw
-rwxr-xr-x	2277	rename_keys	blob \| history \| raw
-rwxr-xr-x	3429	replace_vals	blob \| history \| raw
-rwxr-xr-x	3587	rescan_seq	blob \| history \| raw
-rwxr-xr-x	2067	reverse_seq	blob \| history \| raw
-rwxr-xr-x	1778	scores_to_dec	blob \| history \| raw
-rwxr-xr-x	3024	shred_seq	blob \| history \| raw
-rwxr-xr-x	1616	shuffle_records	blob \| history \| raw
-rwxr-xr-x	2138	shuffle_seq	blob \| history \| raw
-rwxr-xr-x	4804	soap_seq	blob \| history \| raw
-rwxr-xr-x	3058	sort_records	blob \| history \| raw
-rwxr-xr-x	3176	split_bed	blob \| history \| raw
-rwxr-xr-x	2360	split_pair_seq	blob \| history \| raw
-rwxr-xr-x	3259	split_seq	blob \| history \| raw
-rwxr-xr-x	2962	split_vals	blob \| history \| raw
-rwxr-xr-x	3267	substitute_vals	blob \| history \| raw
-rwxr-xr-x	3545	sum_vals	blob \| history \| raw
-rwxr-xr-x	1618	swapcase_seq	blob \| history \| raw
-rwxr-xr-x	2931	tile_seq	blob \| history \| raw
-rwxr-xr-x	2707	translate_seq	blob \| history \| raw
-rwxr-xr-x	2810	transliterate_seq	blob \| history \| raw
-rwxr-xr-x	2982	transliterate_vals	blob \| history \| raw
-rwxr-xr-x	2459	trim_seq	blob \| history \| raw
-rwxr-xr-x	2598	uchime_seq	blob \| history \| raw
-rwxr-xr-x	3009	uclust_seq	blob \| history \| raw
-rwxr-xr-x	3046	uniq_seq	blob \| history \| raw
-rwxr-xr-x	2836	uniq_vals	blob \| history \| raw
-rwxr-xr-x	8804	upload_to_ucsc	blob \| history \| raw
-rwxr-xr-x	1971	uppercase_seq	blob \| history \| raw
-rwxr-xr-x	3292	usearch_seq	blob \| history \| raw
-rwxr-xr-x	8104	vmatch_seq	blob \| history \| raw
-rwxr-xr-x	3217	write_2bit	blob \| history \| raw
-rwxr-xr-x	3575	write_454	blob \| history \| raw
-rwxr-xr-x	3283	write_align	blob \| history \| raw
-rwxr-xr-x	3005	write_bed	blob \| history \| raw
-rwxr-xr-x	4371	write_blast	blob \| history \| raw
-rwxr-xr-x	2547	write_fasta	blob \| history \| raw
-rwxr-xr-x	3317	write_fasta_files	blob \| history \| raw
-rwxr-xr-x	2691	write_fastq	blob \| history \| raw
-rwxr-xr-x	3473	write_fastq_files	blob \| history \| raw
-rwxr-xr-x	3025	write_fixedstep	blob \| history \| raw
-rwxr-xr-x	2805	write_gff	blob \| history \| raw
-rwxr-xr-x	2638	write_kiss	blob \| history \| raw
-rwxr-xr-x	10401	write_mysql	blob \| history \| raw
-rwxr-xr-x	2753	write_psl	blob \| history \| raw
-rwxr-xr-x	2254	write_sam	blob \| history \| raw
-rwxr-xr-x	2910	write_solid	blob \| history \| raw
-rwxr-xr-x	4803	write_tab	blob \| history \| raw
-rwxr-xr-x	2480	write_ucsc_config	blob \| history \| raw