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2 parents cea4e55 + 186fdd3 commit 892dec044d226d38a345e2add5ec7f37bdfe6395 @mothur-westcott mothur-westcott committed Apr 5, 2016
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Showing with 218,639 additions and 13,217 deletions.
  1. +17 −0 .travis.yml
  2. +2 −13 INSTALL.md
  3. +16 −48 makefile → Makefile
  4. +532 −465 Mothur.xcodeproj/project.pbxproj
  5. +2 −0 README.md
  6. +192,840 −0 TestMothur/dataset.cpp
  7. +55 −0 TestMothur/dataset.h
  8. +16,034 −0 TestMothur/fastqdataset.cpp
  9. +34 −0 TestMothur/fastqdataset.h
  10. +21 −0 TestMothur/main.cpp
  11. +73 −0 TestMothur/testbiominfocommand.cpp
  12. +29 −0 TestMothur/testbiominfocommand.h
  13. +18 −0 TestMothur/testcommands/testgetgroupscommand.cpp
  14. +34 −0 TestMothur/testcommands/testgetgroupscommand.h
  15. +19 −0 TestMothur/testcommands/testmergegroupscommand.cpp
  16. +26 −0 TestMothur/testcommands/testmergegroupscommand.h
  17. +18 −0 TestMothur/testcommands/testremovegroupscommand.cpp
  18. +34 −0 TestMothur/testcommands/testremovegroupscommand.h
  19. +39 −0 TestMothur/testcommands/testrenameseqscommand.cpp
  20. +40 −0 TestMothur/testcommands/testrenameseqscommand.h
  21. +1 −1 TestMothur/testcommands/testsetseedcommand.cpp
  22. +65 −0 TestMothur/testcontainers/testfastqread.cpp
  23. +32 −0 TestMothur/testcontainers/testfastqread.h
  24. +3 −2 TestMothur/{testdatastructures → testcontainers}/testsequence.cpp
  25. +22 −0 TestMothur/testcontainers/testsequence.h
  26. +118 −0 TestMothur/testvsearchfileparser.cpp
  27. +35 −0 TestMothur/testvsearchfileparser.h
  28. +98 −0 makefile-internal
  29. +4 −190 source/chimera/bellerophon.cpp
  30. +2 −6 source/chimera/bellerophon.h
  31. +8 −170 source/chimera/ccode.cpp
  32. +3 −12 source/chimera/ccode.h
  33. +1 −162 source/chimera/chimeracheckrdp.cpp
  34. +2 −6 source/chimera/chimeracheckrdp.h
  35. +1 −1 source/chimera/chimerarealigner.h
  36. +7 −279 source/chimera/chimeraslayer.cpp
  37. +2 −7 source/chimera/chimeraslayer.h
  38. +1 −1 source/chimera/decalc.cpp
  39. +1 −1 source/chimera/maligner.h
  40. +22 −163 source/chimera/{chimera.cpp → mothurchimera.cpp}
  41. +5 −12 source/chimera/{chimera.h → mothurchimera.h}
  42. +3 −201 source/chimera/pintail.cpp
  43. +3 −7 source/chimera/pintail.h
  44. +1 −1 source/chimera/slayer.h
  45. +63 −247 source/classifier/bayesian.cpp
  46. +7 −130 source/classifier/classify.cpp
  47. +2 −1 source/classifier/classify.h
  48. +159 −61 source/classifier/phylosummary.cpp
  49. +9 −8 source/classifier/phylosummary.h
  50. +64 −179 source/classifier/phylotree.cpp
  51. +4 −4 source/clearcut/cmdargs.cpp
  52. +10 −10 source/clearcut/getopt_long.cpp
  53. +36 −62 source/commandfactory.cpp
  54. +0 −1 source/commandfactory.hpp
  55. +2 −301 source/commands/aligncommand.cpp
  56. +1 −6 source/commands/aligncommand.h
  57. +874 −0 source/commands/biominfocommand.cpp
  58. +58 −0 source/commands/biominfocommand.h
  59. +14 −4 source/commands/catchallcommand.cpp
  60. +2 −29 source/commands/chimerabellerophoncommand.cpp
  61. +2 −2 source/commands/chimerabellerophoncommand.h
  62. +0 −150 source/commands/chimeraccodecommand.cpp
  63. +2 −6 source/commands/chimeraccodecommand.h
  64. +1 −134 source/commands/chimeracheckcommand.cpp
  65. +2 −6 source/commands/chimeracheckcommand.h
  66. +0 −136 source/commands/chimerapintailcommand.cpp
  67. +2 −6 source/commands/chimerapintailcommand.h
  68. +9 −443 source/commands/chimeraslayercommand.cpp
  69. +4 −11 source/commands/chimeraslayercommand.h
  70. +9 −44 source/commands/chimerauchimecommand.cpp
  71. +0 −1 source/commands/chimerauchimecommand.h
  72. +1 −1 source/commands/chopseqscommand.cpp
  73. +43 −71 source/commands/classifyotucommand.cpp
  74. +3 −4 source/commands/classifyotucommand.h
  75. 0 source/commands/classifyrfsharedcommand.cpp
  76. +95 −370 source/commands/classifyseqscommand.cpp
  77. +2 −8 source/commands/classifyseqscommand.h
  78. +418 −164 source/commands/clustercommand.cpp
  79. +4 −1 source/commands/clustercommand.h
  80. +390 −406 source/commands/clustersplitcommand.cpp
  81. +5 −2 source/commands/clustersplitcommand.h
  82. +13 −19 source/commands/collectcommand.cpp
  83. +1 −1 source/commands/countseqscommand.cpp
  84. +87 −47 source/commands/deconvolutecommand.cpp
  85. +1 −1 source/commands/deconvolutecommand.h
  86. +1 −1 source/commands/degapseqscommand.cpp
  87. +1 −599 source/commands/distancecommand.cpp
  88. +1 −16 source/commands/distancecommand.h
  89. +7 −362 source/commands/filterseqscommand.cpp
  90. +5 −5 source/commands/filterseqscommand.h
  91. +27 −1 source/commands/filtersharedcommand.cpp
  92. +43 −3 source/commands/getcurrentcommand.cpp
  93. +2 −2 source/commands/getcurrentcommand.h
  94. +262 −3 source/commands/getgroupscommand.cpp
  95. +7 −1 source/commands/getgroupscommand.h
  96. +7 −5 source/commands/getotulabelscommand.cpp
  97. +2 −2 source/commands/getotulabelscommand.h
  98. +13 −29 source/commands/getoturepcommand.cpp
  99. +174 −103 source/commands/getseqscommand.cpp
  100. +1 −1 source/commands/getseqscommand.h
  101. +73 −20 source/commands/getsharedotucommand.cpp
  102. +4 −2 source/commands/getsharedotucommand.h
  103. +12 −8 source/commands/lefsecommand.cpp
  104. +21 −27 source/commands/listseqscommand.cpp
  105. +1 −1 source/commands/listseqscommand.h
  106. +0 −289 source/commands/loadlogfilecommand.cpp
  107. +0 −47 source/commands/loadlogfilecommand.h
  108. +2 −0 source/commands/makebiomcommand.cpp
  109. +463 −143 source/commands/makecontigscommand.cpp
  110. +816 −430 source/commands/makecontigscommand.h
  111. +11 −19 source/commands/makefastqcommand.cpp
  112. +22 −5 source/commands/makefilecommand.cpp
  113. +1 −0 source/commands/makefilecommand.h
  114. +469 −54 source/commands/mergegroupscommand.cpp
  115. +9 −1 source/commands/mergegroupscommand.h
  116. +3 −3 source/commands/otuhierarchycommand.cpp
  117. +4 −446 source/commands/pairwiseseqscommand.cpp
  118. +0 −6 source/commands/pairwiseseqscommand.h
  119. +83 −191 source/commands/parsefastaqcommand.cpp
  120. +5 −14 source/commands/parsefastaqcommand.h
  121. +19 −33 source/commands/parselistscommand.cpp
  122. +1 −1 source/commands/pcrseqscommand.cpp
  123. +1 −22 source/commands/pipelinepdscommand.cpp
  124. +1 −0 source/commands/preclustercommand.cpp
  125. +3 −4 source/commands/preclustercommand.h
  126. +39 −44 source/commands/rarefactcommand.cpp
  127. +1 −1 source/commands/removedistscommand.cpp
  128. +269 −3 source/commands/removegroupscommand.cpp
  129. +7 −1 source/commands/removegroupscommand.h
  130. +1 −0 source/commands/removelineagecommand.cpp
  131. +4 −4 source/commands/removeotulabelscommand.cpp
  132. +2 −2 source/commands/removeotulabelscommand.h
  133. +134 −71 source/commands/removeseqscommand.cpp
  134. +1 −1 source/commands/removeseqscommand.h
  135. +540 −188 source/commands/renameseqscommand.cpp
  136. +12 −1 source/commands/renameseqscommand.h
  137. +75 −422 source/commands/screenseqscommand.cpp
  138. +3 −7 source/commands/screenseqscommand.h
  139. +299 −452 source/commands/sensspeccommand.cpp
  140. +13 −23 source/commands/sensspeccommand.h
  141. +18 −10 source/commands/seqsummarycommand.cpp
  142. +140 −5 source/commands/setcurrentcommand.cpp
  143. +3 −2 source/commands/setcurrentcommand.h
  144. +1 −1 source/commands/sharedcommand.cpp
  145. +15 −1,585 source/commands/shhhercommand.cpp
  146. +1 −1,263 source/commands/shhhercommand.h
  147. +79 −92 source/commands/splitabundcommand.cpp
  148. +14 −18 source/commands/splitgroupscommand.cpp
  149. +184 −170 source/commands/sracommand.cpp
  150. +1 −1 source/commands/sracommand.h
  151. +35 −41 source/commands/summarycommand.cpp
  152. +1 −1 source/commands/summaryqualcommand.cpp
  153. +109 −9 source/commands/summarytaxcommand.cpp
  154. +4 −1 source/commands/summarytaxcommand.h
  155. +1 −1 source/commands/trimseqscommand.cpp
  156. +9 −76 source/datastructures/alignmentdb.cpp
  157. +63 −10 source/datastructures/counttable.cpp
  158. +4 −2 source/datastructures/counttable.h
  159. +38 −44 source/datastructures/designmap.cpp
  160. +0 −5 source/datastructures/distancedb.hpp
  161. +103 −0 source/datastructures/fastqread.cpp
  162. +17 −2 source/datastructures/fastqread.h
  163. +25 −0 source/datastructures/groupmap.cpp
  164. +1 −1 source/datastructures/groupmap.h
  165. +5 −0 source/datastructures/sequence.hpp
  166. +23 −13 source/datastructures/sharedrabundfloatvector.cpp
  167. +4 −2 source/datastructures/sharedrabundfloatvector.h
  168. +13 −13 source/datastructures/sharedrabundvector.cpp
  169. +2 −3 source/datastructures/sharedrabundvector.h
  170. +1 −1 source/datastructures/sparsedistancematrix.cpp
  171. +1 −3 source/datastructures/tree.cpp
  172. +4 −143 source/engine.cpp
  173. +2 −0 source/linearalgebra.cpp
  174. +2 −23 source/mothur.cpp
  175. +5 −6 source/mothur.h
  176. +488 −427 source/mothurout.cpp
  177. +22 −7 source/mothurout.h
  178. +161 −237 source/read/splitmatrix.cpp
  179. +3 −5 source/read/splitmatrix.h
  180. +3 −4 source/svm/svm.cpp
  181. +4 −1 source/trimoligos.cpp
  182. +7 −7 source/uchime_src/mk
  183. +1 −37 source/validparameter.cpp
  184. +1 −1 source/venn.cpp
  185. +272 −0 source/vsearchfileparser.cpp
  186. +50 −0 source/vsearchfileparser.h
View
17 .travis.yml
@@ -0,0 +1,17 @@
+language: C++
+os:
+ - osx
+ - linux
+
+addons:
+ apt:
+ packages:
+ - libreadline6
+ - libreadline6-dev
+ - libboost-all-dev
+
+before install:
+ - if [[ "TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
+ - if [[ "TRAVIS_OS_NAME" == "osx" ]]; then brew install readline boost; fi
+
+script: make install
View
15 INSTALL.md
@@ -1,7 +1,6 @@
#For Unix / Linux / Centos
-#Current makefile compatible with Boost 1.58.0
-1. Boost requires some things to installed on your machine already. Most come standard on many flavors on Unix, but you may need to install the devel packages. Install libz, bzip2 and python, if its not on your machine, including zlib-devel, bzip2-devel, python-devel.
+1. Boost requires some things to installed on your machine already. Most come standard on many flavors on Unix, but you may need to install the devel packages. Install libz, bzip2 and python, if its not on your machine, including zlib-devel, bzip2-devel.
This can be easily done with yum or apt get.
2. Download Boost, http://www.boost.org
@@ -11,16 +10,6 @@
./bootstrap.sh --prefix=/usr/local/
./b2 install
-4. Edit mothur's makefile to indicate your boost installation location. This should match the setting of --prefix in the boost install.
- #From the boost install
- ./bootstrap.sh --prefix=/usr/local/
-
- #Mothur's makefile
- BOOST_INCLUDE_DIR="/usr/local/include/"
- BOOST_LIBRARY_DIR="/usr/local/lib/"
-
-5. Copy libz.a into BOOST_LIBRARY_DIR.
-
-6. Run make. If you get a linking errors, it is likely because the zlib files were not found correctly. You may need to add gzip.cpp and zlib.cpp to the source folder of mothur. They are located in the boost_versionNumber/libs/iostreams/src/gzip.cpp.
+4. Run make. If you get a linking errors, it is likely because the zlib files were not found correctly. You may need to add gzip.cpp and zlib.cpp to the source folder of mothur. They are located in the boost_versionNumber/libs/iostreams/src/gzip.cpp.
View
64 makefile → Makefile
@@ -8,36 +8,25 @@
# Macros
#
-USEMPI ?= no
64BIT_VERSION ?= yes
+OPTIMIZE ?= yes
USEREADLINE ?= yes
-USECOMPRESSION ?= no
USEBOOST ?= yes
+BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"7/27/2015\""
-VERSION = "\"1.36.1\""
-
-# Optimize to level 3:
-CXXFLAGS += -O3
-
+RELEASE_DATE = "\"4/05/2016\""
+VERSION = "\"1.37.0\""
ifeq ($(strip $(64BIT_VERSION)),yes)
- #if you are a mac user use the following line
- TARGET_ARCH += -arch x86_64
-
- #if you using cygwin to build Windows the following line
- #CXX = x86_64-w64-mingw32-g++
- #CC = x86_64-w64-mingw32-g++
- #TARGET_ARCH += -m64 -static
-
- #if you are a linux user use the following line
- #CXXFLAGS += -mtune=native -march=native
-
CXXFLAGS += -DBIT_VERSION
endif
+# Fastest
+ifeq ($(strip $(OPTIMIZE)),yes)
+ CXXFLAGS += -O3
+endif
-CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -O3
ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
else
@@ -51,38 +40,21 @@ endif
ifeq ($(strip $(USEREADLINE)),yes)
CXXFLAGS += -DUSE_READLINE
- LIBS = \
- -lreadline\
- -lncurses
+ LIBS += -lreadline
endif
-MPICXX ?= mpic++
-ifeq ($(strip $(USEMPI)),yes)
- CXX = $(MPICXX)
- CXXFLAGS += -DUSE_MPI
-endif
#The boost libraries allow you to read gz files.
ifeq ($(strip $(USEBOOST)),yes)
- BOOST_INCLUDE_DIR="/usr/local/include"
- BOOST_LIBRARY_DIR="/usr/local/lib"
-
- CXXFLAGS += -DUSE_BOOST
- LIBS += \
- ${BOOST_LIBRARY_DIR}/libboost_iostreams.a \
- ${BOOST_LIBRARY_DIR}/zlib.a
-
- #if linux or windows then ${BOOST_LIBRARY_DIR}/libz.a
+#User specified boost library path
+ifeq ($(strip $(BOOST_LIBRARY_DIR)),"\"Enter_your_boost_library_path_here\"")
+else
+ LDFLAGS += ${BOOST_LIBRARY_DIR}
endif
-
-# if you want to enable reading and writing of compressed files, set to yes.
-# The default is no. this may only work on unix-like systems, not for windows.
-
-
-ifeq ($(strip $(USECOMPRESSION)),yes)
- CXXFLAGS += -DUSE_COMPRESSION
+ LIBS += -lboost_iostreams -lz
+ CXXFLAGS += -DUSE_BOOST
endif
#
@@ -108,13 +80,10 @@ endif
mothur : $(OBJECTS) uchime
$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
- strip mothur
-
uchime:
cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
-
install : mothur
@@ -130,4 +99,3 @@ install : mothur
clean :
@rm -f $(OBJECTS)
@rm -f uchime
-
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997 Mothur.xcodeproj/project.pbxproj 100644 → 100755

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2 README.md
@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.org/mothur/mothur.svg?branch=v.1.37.0)](https://travis-ci.org/mothur/mothur)
+
# README
Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. mothur is available under the GPL license.
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