added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / Mothur.xcodeproj / project.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 0594ef6564bfc1d7f250071faef94646f185e7b1..e2673fc9331524944d0b8b3553e00c42a1f34766 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -37,6 +37,8 @@
                A71D924511AEB42400D00CBC /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = "<group>"; };
                A71D924611AEB42400D00CBC /* splitmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitmatrix.cpp; sourceTree = "<group>"; };
                A71D924711AEB42400D00CBC /* splitmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitmatrix.h; sourceTree = "<group>"; };
+               A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsefastaqcommand.h; sourceTree = "<group>"; };
+               A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsefastaqcommand.cpp; sourceTree = "<group>"; };
                A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = "<group>"; };
                A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
                A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
@@ -49,7 +51,10 @@
                A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = "<group>"; };
                A747E81C116365E000FB9042 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = "<group>"; };
                A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = "<group>"; };
+               A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterfragmentscommand.h; sourceTree = "<group>"; };
+               A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterfragmentscommand.cpp; sourceTree = "<group>"; };
                A7639F8D1175DF35008F5578 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+               A768D95D1248FEAA008AB1D0 /* mothur */ = {isa = PBXFileReference; lastKnownFileType = "compiled.mach-o.executable"; path = mothur; sourceTree = "<group>"; };
                A76AAD02117F322B003D8DA1 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = "<group>"; };
                A76AAD03117F322B003D8DA1 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
                A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; };
@@ -61,6 +66,10 @@
                A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
                A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
                A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+               A787A24F124CB46C0076EB84 /* getlineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlineagecommand.h; sourceTree = "<group>"; };
+               A787A250124CB46C0076EB84 /* getlineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlineagecommand.cpp; sourceTree = "<group>"; };
+               A787A28E124CE1470076EB84 /* removelineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removelineagecommand.h; sourceTree = "<group>"; };
+               A787A28F124CE1470076EB84 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = "<group>"; };
                A798626D1240D91B005FC847 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = "<group>"; };
                A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = "<group>"; };
                A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
@@ -486,15 +495,21 @@
                A7DF0AE2121EBB14004A03EA /* prng.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = prng.h; sourceTree = "<group>"; };
                A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsesffcommand.cpp; sourceTree = "<group>"; };
                A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = "<group>"; };
+               A7F139481247C3CB0033324C /* splitgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitgroupscommand.h; sourceTree = "<group>"; };
+               A7F139491247C3CB0033324C /* splitgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitgroupscommand.cpp; sourceTree = "<group>"; };
                A7F6C8E1124229F900299875 /* fisher2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = fisher2.c; sourceTree = "<group>"; };
                A7F6C8E2124229F900299875 /* fisher2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fisher2.h; sourceTree = "<group>"; };
                A7F6C8E3124229F900299875 /* metastats2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = metastats2.c; sourceTree = "<group>"; };
+               A7F6C8EA12423C0300299875 /* metastatscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastatscommand.h; sourceTree = "<group>"; };
+               A7F6C8EB12423C0300299875 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = "<group>"; };
+               A7F6C9D512425D4600299875 /* metastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastats.h; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
 /* Begin PBXGroup section */
                08FB7794FE84155DC02AAC07 /* mothur */ = {
                        isa = PBXGroup;
                        children = (
+                               A768D95D1248FEAA008AB1D0 /* mothur */,
                                A7639F8D1175DF35008F5578 /* makefile */,
                                A7DA1FF0113FECD400BF472F /* alignment.cpp */,
                                A7DA1FF1113FECD400BF472F /* alignment.hpp */,
@@ -741,6 +756,8 @@
                                A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
                                A7DA2021113FECD400BF472F /* clustercommand.cpp */,
                                A7DA2022113FECD400BF472F /* clustercommand.h */,
+                               A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */,
+                               A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */,
                                A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
                                A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
                                A7DA2026113FECD400BF472F /* collectcommand.h */,
@@ -761,6 +778,8 @@
                                A7DA205B113FECD400BF472F /* getgroupcommand.h */,
                                A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
                                A7DA205D113FECD400BF472F /* getlabelcommand.h */,
+                               A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
+                               A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
                                A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
                                A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
                                A7DA2061113FECD400BF472F /* getoturepcommand.h */,
@@ -783,8 +802,8 @@
                                A7DA207D113FECD400BF472F /* heatmapsimcommand.h */,
                                A7DA207E113FECD400BF472F /* helpcommand.cpp */,
                                A7DA207F113FECD400BF472F /* helpcommand.h */,
-                               A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
                                A7DA208E113FECD400BF472F /* libshuffcommand.h */,
+                               A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
                                A7DA2090113FECD400BF472F /* listseqscommand.h */,
                                A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
                                A703FE931194645F002C397E /* makegroupcommand.h */,
@@ -793,6 +812,8 @@
                                A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
                                A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
                                A7DA209B113FECD400BF472F /* mergefilecommand.h */,
+                               A7F6C8EA12423C0300299875 /* metastatscommand.h */,
+                               A7F6C8EB12423C0300299875 /* metastatscommand.cpp */,
                                A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
                                A7DA209D113FECD400BF472F /* mgclustercommand.h */,
                                A7DA20AC113FECD400BF472F /* nocommands.cpp */,
@@ -801,10 +822,12 @@
                                A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
                                A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
                                A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
+                               A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */,
+                               A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */,
                                A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
                                A7DA20BD113FECD400BF472F /* parselistscommand.h */,
-                               A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
                                A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
+                               A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
                                A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
                                A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
                                A7DA20C3113FECD400BF472F /* pcacommand.h */,
@@ -827,6 +850,8 @@
                                A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
                                A7DA20F1113FECD400BF472F /* readtreecommand.h */,
                                A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+                               A787A28E124CE1470076EB84 /* removelineagecommand.h */,
+                               A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
                                A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
                                A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
                                A7DA20F5113FECD400BF472F /* reversecommand.h */,
@@ -851,6 +876,8 @@
                                A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
                                A71D924511AEB42400D00CBC /* splitabundcommand.h */,
                                A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
+                               A7F139481247C3CB0033324C /* splitgroupscommand.h */,
+                               A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
                                A7DA2155113FECD400BF472F /* summarycommand.h */,
                                A7DA2154113FECD400BF472F /* summarycommand.cpp */,
                                A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
@@ -1040,6 +1067,7 @@
                        children = (
                                A7F6C8E2124229F900299875 /* fisher2.h */,
                                A7F6C8E1124229F900299875 /* fisher2.c */,
+                               A7F6C9D512425D4600299875 /* metastats.h */,
                                A7F6C8E3124229F900299875 /* metastats2.c */,
                        );
                        name = metastatsource;