Initial commit with the first release

grev-uv · Jul 20, 2017 · 6133eec · 6133eec
1 parent 806e83e
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diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
@@ -0,0 +1,42 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "/usr/include",
+                "/usr/lib/syslinux/com32/include",
+                "/usr/lib/gcc/x86_64-linux-gnu/4.8/include",
+                "/usr/lib/syslinux/com32/include",
+                "/usr/lib/jvm/java-8-openjdk-amd64/include",
+                "/usr/lib/jvm/java-7-openjdk-amd64/include",
+                "/usr/src/linux-headers-4.2.0-27/arch/x86/include",
+                "/usr/src/linux-headers-4.2.0-27/include",
+                "/usr/src/linux-headers-4.2.0-27-generic/arch/x86/include",
+                "/usr/src/linux-headers-4.2.0-27-generic/include",
+                "lib/common-libs",
+                "lib/bioinfo-libs"
+            ],
+            "browse": {
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": "",
+                "path": [
+                    "/usr/include",
+                    "/usr/lib/syslinux/com32/include",
+                    "/usr/lib/gcc/x86_64-linux-gnu/4.8/include",
+                    "/usr/lib/syslinux/com32/include",
+                    "/usr/lib/jvm/java-8-openjdk-amd64/include",
+                    "/usr/lib/jvm/java-7-openjdk-amd64/include",
+                    "/usr/src/linux-headers-4.2.0-27/arch/x86/include",
+                    "/usr/src/linux-headers-4.2.0-27/include",
+                    "/usr/src/linux-headers-4.2.0-27-generic/arch/x86/include",
+                    "/usr/src/linux-headers-4.2.0-27-generic/include",
+                    "lib/common-libs",
+                    "lib/bioinfo-libs",
+                    "${workspaceRoot}"
+                ]
+            },
+            "intelliSenseMode": "clang-x64"
+        }
+    ],
+    "version": 2
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -0,0 +1,102 @@
+{
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "1 thread",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceRoot}/bin/hpg-hmapper",
+      "args": [
+        "-mc", "/home/cesar/Documentos/hpg-support/hmc_test_data/mc_alignments.bam",
+        "-hmc", "/home/cesar/Documentos/hpg-support/hmc_test_data/hmc_alignments.bam",
+        //"-t",
+        "-i","/genome/index_bs_previous",
+        "--mc-methyl-stats-file","/home/cesar/Documentos/hpg-support/hmc_test_data/mc_methyl_stats.bin",
+        "--hmc-methyl-stats-file","/home/cesar/Documentos/hpg-support/hmc_test_data/hmc_methyl_stats.bin",
+        "--cpu-threads", "1",
+        "-o","/home/cesar/Documentos/hpg-support/hmc_test_data/out/",
+        "--memory","30G",
+        "--batch-size","1000000",
+        "--output-format","csv"
+      ],
+      "stopAtEntry": true,
+      "cwd": "${workspaceRoot}",
+      "environment": [],
+      "externalConsole": false,
+      "linux": {
+        "MIMode": "gdb"
+      }
+    },
+    {
+      "name": "3 threads",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceRoot}/bin/hpg-hmapper",
+      "args": [
+        "-mc", "/home/cesar/Documentos/hpg-support/hmc_test_data/mc_alignments.bam",
+        "-hmc", "/home/cesar/Documentos/hpg-support/hmc_test_data/hmc_alignments.bam",
+        "--cpu-threads", "3",
+        "-o","/home/cesar/Documentos/hpg-support/hmc_test_data/out/",
+        "--memory","30G",
+        "--batch-size","100000"
+      ],
+      "stopAtEntry": true,
+      "cwd": "${workspaceRoot}",
+      "environment": [],
+      "externalConsole": false,
+      "linux": {
+        "MIMode": "gdb"
+      }
+    },
+    {
+      "name": "4 threads",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceRoot}/bin/hpg-hmapper",
+      "args": [
+        "-mc", "/home/cesar/Documentos/hpg-support/hmc_test_data/mc_alignments.bam",
+        "-hmc", "/home/cesar/Documentos/hpg-support/hmc_test_data/hmc_alignments.bam",
+        //"-t",
+        "-i","/genome/index_bs_previous",
+        "--mc-methyl-stats-file","/home/cesar/Documentos/hpg-support/hmc_test_data/mc_methyl_stats.bin",
+        "--hmc-methyl-stats-file","/home/cesar/Documentos/hpg-support/hmc_test_data/hmc_methyl_stats.bin",
+        "--cpu-threads", "4",
+        "-o","/home/cesar/Documentos/hpg-support/hmc_test_data/out/",
+        "--memory","30G",
+        "--batch-size","4000"
+      ],
+      "stopAtEntry": true,
+      "cwd": "${workspaceRoot}",
+      "environment": [],
+      "externalConsole": false,
+      "linux": {
+        "MIMode": "gdb"
+      }
+    },
+    {
+      "name": "6 threads",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceRoot}/bin/hpg-hmapper",
+      "args": [
+        "-mc", "/home/cesar/Documentos/hpg-support/hmc_test_data/mc_alignments.bam",
+        "-hmc", "/home/cesar/Documentos/hpg-support/hmc_test_data/hmc_alignments.bam",
+        //"-t",
+        "-i","/genome/index_bs_previous",
+        "--mc-methyl-stats-file","/home/cesar/Documentos/hpg-support/hmc_test_data/mc_methyl_stats.bin",
+        "--hmc-methyl-stats-file","/home/cesar/Documentos/hpg-support/hmc_test_data/hmc_methyl_stats.bin",
+        "--cpu-threads", "6",
+        "-o","/home/cesar/Documentos/hpg-support/hmc_test_data/out/",
+        "--memory","30G",
+        "--batch-size","6000"
+      ],
+      "stopAtEntry": true,
+      "cwd": "${workspaceRoot}",
+      "environment": [],
+      "externalConsole": false,
+      "linux": {
+        "MIMode": "gdb"
+      }
+    }
+  ]
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,123 @@
+//-------------------------------------------------------
+// Visual Studio Code environment configuration for the
+// HPG-Methyl project.
+//
+// - Date: 15 / 11 / 2016
+// - Who: Cesar
+{
+    // Original code used a tabspace of 2, keep
+    // it like that.
+    "editor.tabSize": 2,
+    "editor.insertSpaces": true,
+    "search.exclude": {
+        "../bin/": true,
+        "../nuevo/": true,
+        "../antiguo/": true
+    }
+,
+"files.associations": {
+    "SConstruct": "python",
+    "*.cu": "c",
+    "*.cuh": "c",
+    "*h*h*h*h*c*h*h*h*h*h*h*h*h*c*c*c*h*h*h*h*h*h*h*h*h*h*h*h*h*h*h*h*htype_traits": "cpp",
+    "type_traits": "cpp",
+    "*h*h*h*h*h*h*h*h*h*h*h*h*h*h*h*h*h*hchrono": "cpp",
+    "chrono": "cpp",
+    "functional": "cpp",
+    "ratio": "cpp",
+    "tuple": "cpp",
+    "*h*hutility": "cpp",
+    "utility": "cpp",
+    "array": "cpp",
+    "*h*hthread": "cpp",
+    "thread": "cpp",
+    "*h*h*h*h*h*h*c*c*h*h*h*h*h*c*c*h*h*h*h*h*h*h*h*h*h*h*h*h*h*h*harray": "cpp",
+    "initializer_list": "cpp",
+    "producer.h": "c",
+    "genome.h": "c",
+    "consumer.h": "c",
+    "scheduler.h": "c",
+    "worker.h": "c",
+    "thread.h": "c",
+    "alignment.h": "c",
+    "db_postgres.h": "c",
+    "options.h": "c",
+    "parser.h": "c",
+    "ssl.h": "c",
+    "bw_io.h": "c",
+    "razf.h": "c",
+    "array_list.h": "c",
+    "db.h": "c",
+    "httpclient.h": "c",
+    "mtab.h": "c",
+    "sorted_hash.h": "c",
+    "str.h": "c",
+    "vector.h": "c",
+    "wtab.h": "c",
+    "heap.h": "c",
+    "linked_list.h": "c",
+    "curl.h": "c",
+    "tree.h": "c",
+    "x509.h": "c",
+    "c++config.h": "c",
+    "*.h++": "c",
+    "*.c++": "c",
+    "sysinfo.h": "c",
+    "result.h": "c",
+    "vcf_db.h": "c",
+    "vcf_file_structure.h": "c",
+    "vcf_stats.h": "c",
+    "bwt.h": "c",
+    "dna_map_region.h": "c",
+    "region.h": "c",
+    "rna_map_region.h": "c",
+    "stdio2.h": "c",
+    "stdint.h": "c",
+    "types.h": "c",
+    "workflow_scheduler.h": "c",
+    "encoding.h": "c",
+    "ssl3.h": "c",
+    "bam_tags.h": "c",
+    "bam.h": "c",
+    "bcf.h": "c",
+    "bed_file_structure.h": "c",
+    "fastq_gzfile.h": "c",
+    "gff_file_structure.h": "c",
+    "ped_file_structure.h": "c",
+    "static_queue.h": "c",
+    "multi.h": "c",
+    "curses.h": "c",
+    "asn1.h": "c",
+    "buffer.h": "c",
+    "crypto.h": "c",
+    "lhash.h": "c",
+    "objects.h": "c",
+    "pem.h": "c",
+    "pkcs7.h": "c",
+    "pqueue.h": "c",
+    "sha.h": "c",
+    "stack.h": "c",
+    "tls1.h": "c",
+    "x509_vfy.h": "c",
+    "string.h": "c",
+    "move.h": "c",
+    "timing.h": "c",
+    "rpc_msg.h": "c",
+    "hmc_common.h": "c",
+    "bam2bcf.h": "c",
+    "locale_classes.h": "c",
+    "sqlite3.h": "c",
+    "stdio.h": "c",
+    "strings.h": "c",
+    "random.h": "c",
+    "argtable2.h": "c",
+    "libconfig.h": "c",
+    "libpq-fe.h": "c",
+    "hashtable.h": "c",
+    "stl_bvector.h": "c",
+    "stl_tempbuf.h": "c",
+    "stl_vector.h": "c",
+    "bgzf.h": "c",
+    "xmlerror.h": "c"
+}
+}
diff --git a/.vscode/tasks.json b/.vscode/tasks.json
@@ -0,0 +1,99 @@
+//-------------------------------------------------------
+// Visual Studio Code environment configuration for the
+// HPG-Methyl project.
+//
+// - Date: 15 / 11 / 2016
+// - Who: Cesar
+{
+    // Building task for Visual Studio code
+    // Includes:
+    // - Release profile.
+    // - Debug profile.
+    // - Clean command.
+    //
+    // - Date: 15 / 11 / 2016
+    // - Who: Cesar
+    "version": "0.1.0",
+    "isShellCommand": true,
+    "command": "sh",
+    "args": [
+        "-c"
+    ],
+    "showOutput": "always",
+    "suppressTaskName": true,
+
+    // Targets for release, debug, clean and package
+    "tasks":[
+        {
+            "taskName": "Build release",
+            "args": [
+                "scons debug=0"
+            ],
+            // Support for error and warning output
+            "problemMatcher": {
+                "owner": "cpp",
+                "fileLocation": ["relative", "${workspaceRoot}"],
+                "pattern": {
+                    "regexp": "^(.*):(\\d+):(\\d+):\\s+(warning|error):\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "severity": 4,
+                    "message": 5
+                }
+            }
+        },
+        {
+            "taskName": "Build debug",
+            "isBuildCommand": true,
+            "args": [
+                "scons debug=1"
+            ],
+            // Support for error and warning output
+            "problemMatcher": {
+                "owner": "cpp",
+                "fileLocation": ["relative", "${workspaceRoot}"],
+                "pattern": {
+                    "regexp": "^(.*):(\\d+):(\\d+):\\s+(warning|error):\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "severity": 4,
+                    "message": 5
+                }
+            }
+        },
+        {
+            "taskName": "Clean project",
+            "args": [
+                "scons -c"
+            ]
+        },
+        {
+            "taskName": "Clean RTL tables",
+            "args": [
+                "find . -type f -name '*.expand' -delete"
+            ]
+        },
+        {
+            "taskName": "Create release packages",
+            "args":[
+                "scons package=1"
+            ]
+        },
+        {
+            "taskName": "Verify build against trunk version (simulated)",
+            "isTestCommand": true,
+            "args":[
+                "/home/cesar/Documentos/hpg-test-bam/test_bam_simulated"
+            ]
+        },
+        {
+            "taskName": "Verify build against trunk version (real)",
+            "isTestCommand": true,
+            "args":[
+                "/home/cesar/Documentos/hpg-test-bam/test_bam_real"
+            ]
+        }
+    ]
+}