rbbt-util 5.44.1 → 6.0.4

data/share/software/opt/ssw/ssw.h

@@ -0,0 +1,130 @@
+/*
+ *  ssw.h
+ *
+ *  Created by Mengyao Zhao on 6/22/10.
+ *  Copyright 2010 Boston College. All rights reserved.
+ *	Version 0.1.4
+ *	Last revision by Mengyao Zhao on 01/30/13.
+ *
+ */
+
+#ifndef SSW_H
+#define SSW_H
+
+#include <stdio.h>
+#include <stdint.h>
+#include <string.h>
+#include <emmintrin.h>
+
+/*!	@typedef	structure of the query profile	*/
+struct _profile;
+typedef struct _profile s_profile;
+
+/*!	@typedef	structure of the alignment result
+	@field	score1	the best alignment score
+	@field	score2	sub-optimal alignment score
+	@field	ref_begin1	0-based best alignment beginning position on reference;	ref_begin1 = -1 when the best alignment beginning 
+						position is not available
+	@field	ref_end1	0-based best alignment ending position on reference
+	@field	read_begin1	0-based best alignment beginning position on read; read_begin1 = -1 when the best alignment beginning 
+						position is not available
+	@field	read_end1	0-based best alignment ending position on read
+	@field	read_end2	0-based sub-optimal alignment ending position on read
+	@field	cigar	best alignment cigar; stored the same as that in BAM format, high 28 bits: length, low 4 bits: M/I/D (0/1/2); 
+					cigar = 0 when the best alignment path is not available
+	@field	cigarLen	length of the cigar string; cigarLen = 0 when the best alignment path is not available
+*/
+typedef struct {
+	uint16_t score1;	
+	uint16_t score2;	
+	int32_t ref_begin1;	
+	int32_t ref_end1;	
+	int32_t	read_begin1;	
+	int32_t read_end1;	
+	int32_t ref_end2;
+	uint32_t* cigar;	
+	int32_t cigarLen;	
+} s_align;
+
+#ifdef __cplusplus
+extern "C" {
+#endif	// __cplusplus
+
+/*!	@function	Create the query profile using the query sequence.
+	@param	read	pointer to the query sequence; the query sequence needs to be numbers
+	@param	readLen	length of the query sequence
+	@param	mat	pointer to the substitution matrix; mat needs to be corresponding to the read sequence
+	@param	n	the square root of the number of elements in mat (mat has n*n elements)
+	@param	score_size	estimated Smith-Waterman score; if your estimated best alignment score is surely < 255 please set 0; if 
+						your estimated best alignment score >= 255, please set 1; if you don't know, please set 2 
+	@return	pointer to the query profile structure
+	@note	example for parameter read and mat:
+			If the query sequence is: ACGTATC, the sequence that read points to can be: 1234142
+			Then if the penalty for match is 2 and for mismatch is -2, the substitution matrix of parameter mat will be:
+			//A  C  G  T  
+			  2 -2 -2 -2 //A
+			 -2  2 -2 -2 //C
+			 -2 -2  2 -2 //G
+			 -2 -2 -2  2 //T
+			mat is the pointer to the array {2, -2, -2, -2, -2, 2, -2, -2, -2, -2, 2, -2, -2, -2, -2, 2}
+*/
+s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size);
+
+/*!	@function	Release the memory allocated by function ssw_init.
+	@param	p	pointer to the query profile structure	
+*/
+void init_destroy (s_profile* p);
+
+// @function	ssw alignment.
+/*!	@function	Do Striped Smith-Waterman alignment.
+	@param	prof	pointer to the query profile structure
+	@param	ref	pointer to the target sequence; the target sequence needs to be numbers and corresponding to the mat parameter of
+				function ssw_init
+	@param	refLen	length of the target sequence
+	@param	weight_gapO	the absolute value of gap open penalty  
+	@param	weight_gapE	the absolute value of gap extension penalty
+	@param	flag	bitwise FLAG; (from high to low) bit 5: when setted as 1, function ssw_align will return the best alignment 
+					beginning position; bit 6: when setted as 1, if (ref_end1 - ref_begin1 < filterd && read_end1 - read_begin1 
+					< filterd), (whatever bit 5 is setted) the function will return the best alignment beginning position and 
+					cigar; bit 7: when setted as 1, if the best alignment score >= filters, (whatever bit 5 is setted) the function
+  					will return the best alignment beginning position and cigar; bit 8: when setted as 1, (whatever bit 5, 6 or 7 is
+ 					setted) the function will always return the best alignment beginning position and cigar. When flag == 0, only 
+					the optimal and sub-optimal scores and the optimal alignment ending position will be returned.
+	@param	filters	score filter: when bit 7 of flag is setted as 1 and bit 8 is setted as 0, filters will be used (Please check the
+ 					decription of the flag parameter for detailed usage.)
+	@param	filterd	distance filter: when bit 6 of flag is setted as 1 and bit 8 is setted as 0, filterd will be used (Please check 
+					the decription of the flag parameter for detailed usage.)
+	@param	maskLen	The distance between the optimal and suboptimal alignment ending position >= maskLen. We suggest to use 
+					readLen/2, if you don't have special concerns. Note: maskLen has to be >= 15, otherwise this function will NOT 
+					return the suboptimal alignment information. Detailed description of maskLen: After locating the optimal
+					alignment ending position, the suboptimal alignment score can be heuristically found by checking the second 
+					largest score in the array that contains the maximal score of each column of the SW matrix. In order to avoid 
+					picking the scores that belong to the alignments sharing the partial best alignment, SSW C library masks the 
+					reference loci nearby (mask length = maskLen) the best alignment ending position and locates the second largest 
+					score from the unmasked elements.
+	@return	pointer to the alignment result structure 
+	@note	Whatever the parameter flag is setted, this function will at least return the optimal and sub-optimal alignment score,
+			and the optimal alignment ending positions on target and query sequences. If both bit 6 and 7 of the flag are setted
+			while bit 8 is not, the function will return cigar only when both criteria are fulfilled. All returned positions are 
+			0-based coordinate.  	
+*/
+s_align* ssw_align (const s_profile* prof, 
+					const int8_t* ref, 
+					int32_t refLen, 
+					const uint8_t weight_gapO, 
+					const uint8_t weight_gapE, 
+					const uint8_t flag,	
+					const uint16_t filters,
+					const int32_t filterd,
+					const int32_t maskLen);
+
+/*!	@function	Release the memory allocated by function ssw_align.
+	@param	a	pointer to the alignment result structure
+*/
+void align_destroy (s_align* a);
+
+#ifdef __cplusplus
+}
+#endif	// __cplusplus
+
+#endif	// SSW_H

data/share/workflow_config.ru

@@ -28,14 +28,14 @@ require Rbbt.etc['app.d/init.rb'].find
 
 #{{{ Workflow
 workflow = Rbbt.etc['target_workflow'].read
-wf = Workflow.require_workflow workflow, true
+wf = Workflow.require_workflow workflow
 
 
 $title = wf.to_s
 $app_name = app_name = wf.to_s + "REST"
 $app = app = eval "class #{app_name} < Sinatra::Base; self end"
 
-Rbbt.search_paths = Path::SEARCH_PATHS.merge(:workflow => File.join(wf.libdir, '{TOPLEVEL}','{SUBPATH}'))
+Rbbt.search_paths = Path::path_maps.merge(:workflow => File.join(wf.libdir, '{TOPLEVEL}','{SUBPATH}'))
 
 etc_dir = Rbbt.etc
 
@@ -143,7 +143,7 @@ app.get '/reload_workflow' do
       end
       load wf_file
   rescue Exception
-      if File.exists?(Rbbt.etc['target_workflow'].read.strip)
+      if File.exist?(Rbbt.etc['target_workflow'].read.strip)
           load Rbbt.etc['target_workflow'].read.strip
       else
           raise $!

metadata

@@ -1,15 +1,28 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.44.1
+  version: 6.0.4
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-12-10 00:00:00.000000000 Z
+date: 2025-03-31 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: scout-gear
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -174,6 +187,7 @@ files:
 - lib/rbbt.rb
 - lib/rbbt/annotations.rb
 - lib/rbbt/annotations/annotated_array.rb
+- lib/rbbt/annotations/refactor.rb
 - lib/rbbt/annotations/util.rb
 - lib/rbbt/association.rb
 - lib/rbbt/association/database.rb
@@ -183,6 +197,7 @@ files:
 - lib/rbbt/association/util.rb
 - lib/rbbt/entity.rb
 - lib/rbbt/entity/identifiers.rb
+- lib/rbbt/entity/refactor.rb
 - lib/rbbt/fix_width_table.rb
 - lib/rbbt/hpc.rb
 - lib/rbbt/hpc/batch.rb
@@ -204,6 +219,7 @@ files:
 - lib/rbbt/monitor.rb
 - lib/rbbt/packed_index.rb
 - lib/rbbt/persist.rb
+- lib/rbbt/persist/refactor.rb
 - lib/rbbt/persist/tsv.rb
 - lib/rbbt/persist/tsv/adapter.rb
 - lib/rbbt/persist/tsv/cdb.rb
@@ -215,8 +231,10 @@ files:
 - lib/rbbt/persist/tsv/sharder.rb
 - lib/rbbt/persist/tsv/tokyocabinet.rb
 - lib/rbbt/persist/tsv/tokyocabinet/marshal.rb
+- lib/rbbt/refactor.rb
 - lib/rbbt/resource.rb
 - lib/rbbt/resource/path.rb
+- lib/rbbt/resource/path/refactor.rb
 - lib/rbbt/resource/rake.rb
 - lib/rbbt/resource/util.rb
 - lib/rbbt/resource/with_key.rb
@@ -239,6 +257,7 @@ files:
 - lib/rbbt/tsv/parallel/through.rb
 - lib/rbbt/tsv/parallel/traverse.rb
 - lib/rbbt/tsv/parser.rb
+- lib/rbbt/tsv/refactor.rb
 - lib/rbbt/tsv/serializers.rb
 - lib/rbbt/tsv/stream.rb
 - lib/rbbt/tsv/util.rb
@@ -252,6 +271,7 @@ files:
 - lib/rbbt/util/colorize.rb
 - lib/rbbt/util/concurrency.rb
 - lib/rbbt/util/concurrency/processes.rb
+- lib/rbbt/util/concurrency/processes/refactor.rb
 - lib/rbbt/util/concurrency/processes/socket.rb
 - lib/rbbt/util/concurrency/processes/worker.rb
 - lib/rbbt/util/concurrency/threads.rb
@@ -259,10 +279,12 @@ files:
 - lib/rbbt/util/docker.rb
 - lib/rbbt/util/excel2tsv.rb
 - lib/rbbt/util/filecache.rb
+- lib/rbbt/util/iruby.rb
 - lib/rbbt/util/log.rb
 - lib/rbbt/util/log/progress.rb
 - lib/rbbt/util/log/progress/report.rb
 - lib/rbbt/util/log/progress/util.rb
+- lib/rbbt/util/log/refactor.rb
 - lib/rbbt/util/migrate.rb
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/misc/annotated_module.rb
@@ -282,13 +304,19 @@ files:
 - lib/rbbt/util/misc/omics.rb
 - lib/rbbt/util/misc/options.rb
 - lib/rbbt/util/misc/pipes.rb
+- lib/rbbt/util/misc/refactor.rb
 - lib/rbbt/util/misc/serialize.rb
 - lib/rbbt/util/misc/ssw.rb
 - lib/rbbt/util/misc/system.rb
 - lib/rbbt/util/named_array.rb
+- lib/rbbt/util/named_array/refactor.rb
 - lib/rbbt/util/open.rb
+- lib/rbbt/util/open/refactor.rb
 - lib/rbbt/util/procpath.rb
 - lib/rbbt/util/python.rb
+- lib/rbbt/util/python/paths.rb
+- lib/rbbt/util/python/run.rb
+- lib/rbbt/util/python/script.rb
 - lib/rbbt/util/python/step.rb
 - lib/rbbt/util/python/util.rb
 - lib/rbbt/util/semaphore.rb
@@ -300,6 +328,7 @@ files:
 - lib/rbbt/util/simpleopt/parse.rb
 - lib/rbbt/util/simpleopt/setup.rb
 - lib/rbbt/util/ssh.rb
+- lib/rbbt/util/ssh/refactor.rb
 - lib/rbbt/util/tar.rb
 - lib/rbbt/util/task/job.rb
 - lib/rbbt/util/tc_cache.rb
@@ -316,6 +345,12 @@ files:
 - lib/rbbt/workflow/integration/ansible/workflow.rb
 - lib/rbbt/workflow/integration/cromwell.rb
 - lib/rbbt/workflow/integration/nextflow.rb
+- lib/rbbt/workflow/refactor.rb
+- lib/rbbt/workflow/refactor/entity.rb
+- lib/rbbt/workflow/refactor/export.rb
+- lib/rbbt/workflow/refactor/inputs.rb
+- lib/rbbt/workflow/refactor/recursive.rb
+- lib/rbbt/workflow/refactor/task_info.rb
 - lib/rbbt/workflow/remote_workflow.rb
 - lib/rbbt/workflow/remote_workflow/driver.rb
 - lib/rbbt/workflow/remote_workflow/driver/rest.rb
@@ -340,6 +375,9 @@ files:
 - lib/rbbt/workflow/util/provenance.rb
 - lib/rbbt/workflow/util/trace.rb
 - python/rbbt/__init__.py
+- python/rbbt/workflow.py
+- python/rbbt/workflow/remote.py
+- python/test.py
 - share/Rlib/plot.R
 - share/Rlib/svg.R
 - share/Rlib/util.R
@@ -452,17 +490,19 @@ files:
 - share/rbbt_commands/workflow/remote/add
 - share/rbbt_commands/workflow/remote/list
 - share/rbbt_commands/workflow/remote/remove
+- share/rbbt_commands/workflow/retry
 - share/rbbt_commands/workflow/server
 - share/rbbt_commands/workflow/task
 - share/rbbt_commands/workflow/trace
 - share/rbbt_commands/workflow/write_info
+- share/software/opt/ssw/ssw.c
+- share/software/opt/ssw/ssw.h
 - share/unicorn.rb
 - share/workflow_config.ru
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -477,8 +517,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.23
-signing_key: 
+rubygems_version: 3.6.5
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files: []