init code space

.gitignore

@@ -30,3 +30,9 @@
 *.exe
 *.out
 *.app
+
+.idea
+cmake-build-debug/
+build
+htslib
+bin

CMakeLists.txt

@@ -0,0 +1,136 @@
+cmake_minimum_required(VERSION 2.8.4)
+project(freemuxlet)
+
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -pthread")
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin")
+
+
+include(ExternalProject)
+ExternalProject_Add(HTSLIB
+        PREFIX ${CMAKE_CURRENT_SOURCE_DIR}/build
+        STAMP_DIR ${CMAKE_CURRENT_SOURCE_DIR}/build/stamp
+        GIT_REPOSITORY https://github.com/samtools/htslib.git
+        GIT_TAG "master"
+        UPDATE_COMMAND ""
+        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/htslib
+        CONFIGURE_COMMAND autoheader && autoconf && ${CMAKE_CURRENT_SOURCE_DIR}/htslib/configure --prefix=${CMAKE_CURRENT_SOURCE_DIR}/htslib --disable-lzma
+        BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/htslib
+        BUILD_COMMAND make && make test
+        )
+
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/htslib/include/)
+
+add_executable(freemuxlet
+        allele.cpp
+        allele.h
+        bam_endian.h
+        bam_ordered_reader.cpp
+        bam_ordered_reader.h
+        bcf_chunked_reader.cpp
+        bcf_chunked_reader.h
+        bcf_filter_arg.h
+        bcf_filtered_reader.cpp
+        bcf_filtered_reader.h
+        bcf_variant_key.h
+        bgzf.h
+        bh_tsne.cpp
+        bh_tsne.h
+        cmd_cram_demuxlet.cpp
+        cmd_cram_digital_pileup.cpp
+        cmd_cram_freemuxlet.cpp
+        cmd_cram_gtf_util.cpp
+        cmd_cram_mux_pileup.cpp
+        cmd_cram_simuxlet.cpp
+        cmd_plp_find_mux_clust.cpp
+        cmd_plp_make_dge_matrix.cpp
+        cmd_sc_kallisto_count.cpp
+        cmd_sc_map_stamps.cpp
+        cmd_sc_multinom_em.cpp
+        cmd_sc_multinom_gibbs.cpp
+        commands.cpp
+        commands.h
+        config.h
+        Constant.h
+        cramore.cpp
+        cramore.h
+        discrete_log_helper.h
+        dropseq.cpp
+        dropseq.h
+        Error.cpp
+        Error.h
+        filter.cpp
+        filter.h
+        genome_interval.cpp
+        genome_interval.h
+        genomeChunk.cpp
+        genomeChunk.h
+        genomeLoci.h
+        gtf.cpp
+        gtf.h
+        gtf_interval_tree.h
+        hts_utils.cpp
+        hts_utils.h
+        interval.cpp
+        interval.h
+        interval_tree.cpp
+        interval_tree.h
+        IO.cpp
+        IO.h
+        knetfile.h
+        ksort.h
+        kstring.h
+        log_tool.cpp
+        log_tool.h
+        louvain.h
+        params.cpp
+        params.h
+        pException.h
+        PhredHelper.cpp
+        PhredHelper.h
+        reference_sequence.cpp
+        reference_sequence.h
+        sam_filtered_reader.cpp
+        sam_filtered_reader.h
+        sam_ordered_writer.cpp
+        sam_ordered_writer.h
+        sc_drop_seq.cpp
+        sc_drop_seq.h
+        sptree.cpp
+        sptree.h
+        tcf.h
+        tsv_reader.cpp
+        tsv_reader.h
+        utils.cpp
+        utils.h
+        variant.cpp
+        variant.h
+        variant_manip.cpp
+        variant_manip.h
+        vntr.cpp
+        vntr.h
+        vptree.h
+        )
+add_dependencies(freemuxlet HTSLIB)
+
+find_library(ZLIB z HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
+if(NOT ZLIB)
+    message(FATAL_ERROR "libz library not found")
+endif()
+
+find_library(CURLLIB curl HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
+if(NOT CURLLIB)
+    message(FATAL_ERROR "libcurl library not found")
+endif()
+
+find_library(BZ2LIB bz2 HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
+if(NOT BZ2LIB)
+    message(FATAL_ERROR "libbz2 library not found")
+endif()
+
+find_library(CRYPTOLIB crypto HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
+if(NOT CRYPTOLIB)
+    message(FATAL_ERROR "libcrypto library not found")
+endif()
+
+target_link_libraries(freemuxlet ${CMAKE_CURRENT_SOURCE_DIR}/htslib/libhts.a ${ZLIB} ${BZ2LIB} ${CURLLIB} ${CRYPTOLIB})

Constant.h

@@ -0,0 +1,60 @@
+/*
+ *  Copyright (C) 2010  Regents of the University of Michigan
+ *
+ *   This program is free software: you can redistribute it and/or modify
+ *   it under the terms of the GNU General Public License as published by
+ *   the Free Software Foundation, either version 3 of the License, or
+ *   (at your option) any later version.
+ *
+ *   This program is distributed in the hope that it will be useful,
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *   GNU General Public License for more details.
+ *
+ *   You should have received a copy of the GNU General Public License
+ *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef _CONSTANT_H_
+#define _CONSTANT_H_
+
+#define  COMPAREFUNC (int (*)(const void *, const void *))
+
+#define  BUFSIZE     1024
+#define  FILENAMELEN 100
+#define  IDLEN       20
+
+#define  SEPARATORS  " \t\n\r\f/"
+#define  WHITESPACE  " \t\n\r\f"
+
+#define  SWTABLESKIP 9
+#define  SWTABLEMAX  10000
+
+#define  _NAN_       ((double) (6.66666e-66))
+
+#define  QTDTDATA    "qtdt.dat"
+#define  QTDTPED     "qtdt.ped"
+#define  QTDTIBD     "qtdt.ibd"
+#define  QTDTRAW     "regress.tbl"
+#define  GENIHDATAIN "genih.dat"
+
+#ifndef  _WIN32
+#define  stricmp     strcasecmp
+#endif
+
+// Constants for older haplotype handling programs
+// Constants for HAPLOXT
+#define XT_MAX_ALLELES  50          // Maximum alleles for crosstabulation
+#define XT_VECTORSIZE   10000       // Total haplotypes in population
+#define XT_POOLTRESH    7           // Threshold for pooling rare alleles
+// Simwalk Haplotype Vectors
+#define HV_MAXSIZE      100         // Haplotypes in single SimWalk pedigree
+#define HV_INFOTRESH    75          // Percentage of loci typed
+#define HV_STATELENGTH  100         // Markers per haplotype
+#define HV_SKIPLINES    4           // lines to skip at bottom of family tree
+// Simwalk Summary Files
+#define HT_TABLE_SIZE   1000
+#define HT_SKIP_LINES   9
+
+#endif
+

Error.cpp

@@ -0,0 +1,126 @@
+/*
+ *  Copyright (C) 2010  Regents of the University of Michigan
+ *
+ *   This program is free software: you can redistribute it and/or modify
+ *   it under the terms of the GNU General Public License as published by
+ *   the Free Software Foundation, either version 3 of the License, or
+ *   (at your option) any later version.
+ *
+ *   This program is distributed in the hope that it will be useful,
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *   GNU General Public License for more details.
+ *
+ *   You should have received a copy of the GNU General Public License
+ *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include "Error.h"
+#include "pException.h"
+
+#include <string>
+#include <cstdio>
+#include <cstdlib>
+#include <ctime>
+#include <stdarg.h>
+
+int32_t globalVerbosityThreshold = 100;
+
+void error(const char * msg, ...)
+{
+  va_list  ap;
+
+  va_start(ap, msg);
+
+  fprintf(stderr, "\nFATAL ERROR - \n");
+  vfprintf(stderr, msg, ap);
+  fprintf(stderr, "\n\n");
+
+  va_end(ap);
+
+  throw pexception;
+  //exit(EXIT_FAILURE);
+}
+
+void warning(const char * msg, ...)
+{
+  va_list  ap;
+
+  va_start(ap, msg);
+
+  time_t current_time;
+  char buff[255];
+  current_time = time(NULL);
+
+  strftime(buff, 120, "%Y/%m/%d %H:%M:%S", localtime(&current_time));
+
+  fprintf(stderr,"\aWARNING [%s] - ", buff);
+  vfprintf(stderr, msg, ap);
+  fprintf(stderr,"\n");
+
+  va_end(ap);
+}
+
+void numerror(const char * msg , ...)
+{
+  va_list  ap;
+
+  va_start(ap, msg);
+
+  fprintf(stderr,"\nFATAL NUMERIC ERROR - ");
+  vfprintf(stderr, msg, ap);
+  fprintf(stderr,"\n\n");
+
+  va_end(ap);
+
+  exit(EXIT_FAILURE);
+}
+
+void notice(const char * msg, ...) {
+  va_list ap;
+  va_start(ap, msg);
+
+  time_t current_time;
+  char buff[255];
+  current_time = time(NULL);
+
+  strftime(buff, 120, "%Y/%m/%d %H:%M:%S", localtime(&current_time));
+
+  fprintf(stderr,"NOTICE [%s] - ", buff);
+  vfprintf(stderr, msg, ap);
+  fprintf(stderr,"\n");
+
+  va_end(ap);
+}
+
+void verbose(int32_t priority, const char * msg, ...) {
+  va_list ap;
+  va_start(ap, msg);
+
+  if ( globalVerbosityThreshold < priority ) {
+    time_t current_time;
+    char buff[255];
+    current_time = time(NULL);
+
+    strftime(buff, 120, "%Y/%m/%d %H:%M:%S", localtime(&current_time));
+
+    fprintf(stderr,"VERBOSE_MESSAGE_%d [%s] - ", priority, buff);
+    vfprintf(stderr, msg, ap);
+    fprintf(stderr,"\n");
+  }
+
+  va_end(ap);
+}
+
+void catprintf(std::string &s, const char * msg, ...)
+{
+  va_list ap;
+
+  va_start(ap, msg);
+
+  char buf[1000];
+  vsprintf(buf, msg, ap);
+
+  s += buf;
+  va_end(ap);
+}

Error.h

@@ -0,0 +1,46 @@
+/*
+ *  Copyright (C) 2010  Regents of the University of Michigan
+ *
+ *   This program is free software: you can redistribute it and/or modify
+ *   it under the terms of the GNU General Public License as published by
+ *   the Free Software Foundation, either version 3 of the License, or
+ *   (at your option) any later version.
+ *
+ *   This program is distributed in the hope that it will be useful,
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *   GNU General Public License for more details.
+ *
+ *   You should have received a copy of the GNU General Public License
+ *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef _ERROR_H_
+#define _ERROR_H_
+
+#include <string>
+
+extern "C" {
+  size_t hts_realloc_or_die(unsigned long, unsigned long, unsigned long, unsigned long, int, void**, char const*);
+}
+
+
+// #ifdef __cplusplus
+// extern "C" {
+// #endif
+
+void error(const char * msg, ...);
+void warning(const char * msg, ...);
+void numerror(const char * msg, ...);
+void notice(const char * msg, ...);
+void verbose(int32_t priority, const char * msg, ...);
+void catprintf(std::string &s, const char * msg, ...);
+
+extern int32_t globalVerbosityThreshold;
+
+// #ifdef __cplusplus
+//   };
+// #endif
+
+
+#endif