71373c60bab25c0cca3564defe0e03574f3b84e2 ceisenhart Wed Oct 21 13:28:18 2015 -0700 Removed a bunch of cruft, two useless files and added some documentation. Refs #16216 diff --git src/hg/expMatrixToJson/expMatrixToJson.c src/hg/expMatrixToJson/expMatrixToJson.c index 51e72fa..c02ded7 100644 --- src/hg/expMatrixToJson/expMatrixToJson.c +++ src/hg/expMatrixToJson/expMatrixToJson.c @@ -1,393 +1,217 @@ /* expData - Takes in an expression matrix and clusters it using a hierarchical agglomerative clustering algorithm. The output defaults to a hierarchichal .json format, with two additional options. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "obscure.h" #include "memalloc.h" #include "jksql.h" #include "expData.h" #include "sqlList.h" #include "hacTree.h" #include "rainbow.h" -boolean clForceLayout = FALSE; // Prints the data in .json format for d3 force layout visualizations boolean clCSV = FALSE; // Converts the comma separated matrix into a tab based file. boolean clMultiThreads = FALSE; // Allows the user to run the program with multiple threads, default is off. int clThreads = 10; // The number of threads to run with the multiThreads option int clMemLim = 4; // The amount of memeory the program can use, read in Gigabytes. -int target = 0; // Used for the target value in rlinkJson. -float longest = 0; // Used to normalize link distances in rlinkJson. +float clLongest = 0; // Used to normalize link distances in rlinkJson. char* clDescFile = NULL; // The user can provide a description file char* clAttributeTable = NULL; // The user can provide an attributes table... this may get removed soon. int nodeCount; //The number of nodes. void usage() /* Explain usage and exit. */ { errAbort( "expMatrixToJson - Takes in an expression matrix and outputs a binary tree clustering the data.\n" " The tree is output as a .json file, a .html file is generated to view the \n" " tree. The files are named using the output argument (ex output.json, output.html).\n" "usage:\n" " expMatrixToJson [options] matrix output\n" "options:\n" " -multiThreads The program will run on multiple threads. \n" - " -forceLayout Prints the output in .json format for d3 forceLayouts. NOTE no .html file will be \n" - " generated using this option.\n" " -CSV The input matrix is in .csv format. \n" " -threads=int Sets the thread count for the multiThreads option, default is 10 \n" " -memLim=int Sets the amount of memeory the program can use before aborting. The default is 4G. \n" + " -verbose=2 Show basic run stats. \n" + " -verbose=3 Show all run stats. Very ugly, avoid at all costs. \n" " -descFile=string The user is providing a description file. The description file must provide a \n" " description for each cell line in the expression matrix. There should be one description per \n" " line, starting on the left side of the expression matrix. The description will appear over a \n" " leaf node when hovered over.\n" - " -verbose=2 Show basic run stats. \n" - " -verbose=3 Show all run stats. \n" ); } /* Command line validation table. */ static struct optionSpec options[] = { {"multiThreads", OPTION_BOOLEAN}, - {"forceLayout", OPTION_BOOLEAN}, {"CSV", OPTION_BOOLEAN}, {"threads", OPTION_INT}, {"memLim", OPTION_INT}, {"descFile", OPTION_STRING}, {"attributeTable", OPTION_STRING}, {NULL, 0}, }; -struct jsonNodeLine -/* Stores the information for a single json node line */ - { - struct jsonNodeLine *next; - char* name; // the source for a given link - double distance; // the distance for a given link - }; - -struct jsonLinkLine -/* Stores the information for a single json link line */ - { - struct jsonLinkLine *next; - int source; // the source for a given link - int target; // the target for a given link - double distance; // the distance for a given link - }; - struct bioExpVector /* Contains expression information for a biosample on many genes. */ { struct bioExpVector *next; char *name; // name of biosample. char *desc; // description of biosample. int count; // Number of genes we have data for. double *vector; // An array allocated dynamically. struct rgbColor color; // Color for this one int children; // Number of bioExpVectors used to build the current }; double stringToDouble(char *s) /* Convert string to a double. Assumes all of string is number - * and aborts on an error. */ + * and aborts on an error. Errors on 'nan'*/ { char* end; double val = strtod(s, &end); if (val != val) errAbort("A value of %f was encountered. Please change this value then re run the program.", val); if ((end == s) || (*end != '\0')) errAbort("invalid double: %s", s); return val; } struct bioExpVector *bioExpVectorListFromFile(char *matrixFile) -// Read a tab-delimited file and return list of bioExpVector. +/* Read a tab-delimited file and return list of bioExpVectors */ { int vectorSize = 0; struct lineFile *lf = lineFileOpen(matrixFile, TRUE); char *line, **row = NULL; struct bioExpVector *list = NULL, *el; while (lineFileNextReal(lf, &line)) { ++nodeCount; if (vectorSize == 0) { // Detect first row. vectorSize = chopByWhite(line, NULL, 0); // counting up AllocArray(row, vectorSize); continue; } AllocVar(el); AllocArray(el->vector, vectorSize); el->count = chopByWhite(line, row, vectorSize); -// assert(el->count == vectorSize); + assert(el->count == vectorSize); int i; for (i = 0; i < el->count; ++i) el->vector[i] = stringToDouble(row[i]); el->children = 1; slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } - int fillInNames(struct bioExpVector *list, char *nameFile) /* Fill in name field from file. */ { struct lineFile *lf = lineFileOpen(nameFile, TRUE); char *line; struct bioExpVector *el = list; int maxSize = 0 ; while (lineFileNextReal(lf, &line)) { if (el == NULL) { warn("More names than items in list"); break; } char *fields[2]; if (strlen(line) > maxSize) maxSize = strlen(line); int fieldCount = chopTabs(line, fields); if (fieldCount >= 1) { el->name = cloneString(fields[0]); if (fieldCount >= 2) el->desc = cloneString(fields[1]); else el->desc = cloneString("0"); } - el = el->next; } - if (el != NULL) errAbort("More items in matrix file than %s", nameFile); - lineFileClose(&lf); return maxSize; } -void printJsonNodeLine(FILE *f, struct jsonNodeLine *node) -{ -fprintf(f," %s\"%s\"%s\"%s\"%s", "{","name", ":", node->name, ","); -fprintf(f,"\"%s\"%s%0.31f%s\n", "y", ":" , node->distance, "},"); -} - -void printEndJsonNodeLine(FILE *f, struct jsonNodeLine *node) -{ -fprintf(f," %s\"%s\"%s\"%s\"%s", "{","name", ":", node->name, ","); -fprintf(f,"\"%s\"%s%0.31f%s\n", "y", ":" , node->distance, "}"); -} - -void printJsonLinkLine(FILE *f, struct jsonLinkLine *links) -/* Prints out a single json link line */ -{ -fprintf(f," %s\"%s\"%s%d%s", "{","source", ":", links->source, ","); -fprintf(f,"\"%s\"%s%d%s", "target", ":" , links->target, ","); -fprintf(f,"\"%s\"%s%0.31f%s\n", "distance", ":" , links->distance , "},"); -} - -void printEndJsonLinkLine(FILE *f, struct jsonLinkLine *links) -/* Prints out a single json link line */ -{ -fprintf(f," %s\"%s\"%s%d%s", "{","source", ":", links->source, ","); -fprintf(f,"\"%s\"%s%d%s", "target", ":" , links->target, ","); -fprintf(f,"\"%s\"%s%0.31f%s\n", "distance", ":" , links->distance , "}"); -} - -void rPrintNodes(FILE *f, struct hacTree *tree, struct jsonNodeLine *nodes) -// Recursively adds the node information to a linked list -{ -char *tissue = ((struct bioExpVector *)(tree->itemOrCluster))->name; -if (tree->childDistance != 0) - // If the current object is a node then we assign no name. - { - struct jsonNodeLine *nNode; - AllocVar(nNode); - nNode->name = " "; - nNode->distance = tree->childDistance; - slAddHead(nodes, nNode); // add the node - } -else { - // Otherwise the current object is a leaf, and the tissue name is printed. - struct jsonNodeLine *lNode; - AllocVar(lNode); - lNode->name = tissue; - lNode->distance = tree->childDistance; - slAddHead(nodes, lNode); // add the node - } - -if (tree->left == NULL && tree->right == NULL) - // Stop at the last element - { - return; - } -else if (tree->left == NULL || tree->right == NULL) - errAbort("\nHow did we get a node with one NULL kid??"); -rPrintNodes(f, tree->left, nodes); -rPrintNodes(f, tree->right, nodes); -} - - -void rPrintLinks(FILE *f, struct hacTree *tree, int source, struct jsonLinkLine *links) -// Recursively loadslist->children = 0 ; the link information into a linked list -{ -if (tree->childDistance > longest) - // the first distance will be the longest, and is used for normalization - longest = tree->childDistance; -if (tree->left == NULL && tree->right == NULL) - // Stop at the last element - { - return; - } -else if (tree->left == NULL || tree->right == NULL) - errAbort("\nHow did we get a node with one NULL kid??"); - -// Left recursion. -struct jsonLinkLine *lLink; -AllocVar(lLink); -++target; -lLink->source = target - 1; // The source and target are always ofset by 1. -lLink->target = target; -lLink->distance = 100*(tree->childDistance/longest); //Calculates the link distance -source = target; // Prepares the source for the right recursion. -slAddHead(links, lLink); // Add the link -rPrintLinks(f, tree->left, source, links); - -// Right recursion. -struct jsonLinkLine *rLink; -AllocVar(rLink); -++target; -rLink->source = source - 1; // The source is dependent on the last target of the left recursion -rLink->target = target; -rLink->distance = 100*(tree->childDistance/longest); -slAddHead(links, rLink); // Add the link -rPrintLinks(f, tree->right, ++source, links); -} - -void printForceLayoutJson(FILE *f, struct hacTree *tree) -// Prints the hacTree into a .json file format for d3 forceLayout visualizations. -{ -// Basic json template for d3 visualizations -fprintf(f,"%s\n", "{"); -fprintf(f," \"%s\"%s\n", "nodes", ":[" ); - -// Print the nodes -struct jsonNodeLine *nodes; -AllocVar(nodes); -rPrintNodes(f, tree, nodes); -slReverse(&nodes); -int nodeCount = slCount(nodes); -int j; -for (j = 0; j < nodeCount -1; ++j) - // iterate through the linked nodelist printing nodes - { - if (j == nodeCount - 2) - printEndJsonNodeLine(f, nodes); - else - { - printJsonNodeLine(f, nodes); - nodes = nodes -> next; - } - } -fprintf(f, "%s\n", "],"); -fprintf(f, "\"%s\"%s\n", "links", ":[" ); - -// Print the links -struct jsonLinkLine *links; -AllocVar(links); -rPrintLinks(f,tree, 0, links); -slReverse(&links); -int linkCount = slCount(links); -int i; -for (i = 0; i< linkCount -1; ++i) - // iterate through the linked linklist printing links - { - if (i == linkCount - 2) - printEndJsonLinkLine(f, links); - else - { - printJsonLinkLine(f, links); - links = links -> next; - } - } -fprintf(f," %s\n", "]"); -fprintf(f,"%s\n", "}"); -} - - static void rAddLeaf(struct hacTree *tree, struct slRef **pList) /* Recursively add leaf to list */ { if (tree->left == NULL && tree->right == NULL) refAdd(pList, tree->itemOrCluster); else { rAddLeaf(tree->left, pList); rAddLeaf(tree->right, pList); } } struct slRef *getOrderedLeafList(struct hacTree *tree) /* Return list of references to bioExpVectors from leaf nodes * ordered by position in hacTree */ { struct slRef *leafList = NULL; rAddLeaf(tree, &leafList); slReverse(&leafList); return leafList; } static void rPrintHierarchicalJson(FILE *f, struct hacTree *tree, int level, double distance) /* Recursively prints out the elements of the hierarchical .json file. */ { struct bioExpVector *bio = (struct bioExpVector *)tree->itemOrCluster; char *tissue = bio->name; struct rgbColor colors = bio->color; -if (tree->childDistance > longest) - // the first distance will be the longest, and is used for normalization - longest = tree->childDistance; +if (tree->childDistance > clLongest) + /* In practice the first distance will be the longest, and is used for normalization. */ + clLongest = tree->childDistance; int i; for (i = 0; i < level; i++) fputc(' ', f); // correct spacing for .json format if (tree->left == NULL && tree->right == NULL) // Print the leaf nodes { if (bio->desc) fprintf(f, "{\"name\":\"%s\",\"kids\":\"%i\",\"distance\":\"%s\",\"colorGroup\":\"rgb(%i,%i,%i)\"}", tissue, 0, bio->desc, colors.r, colors.g, colors.b); else fprintf(f, "{\"name\":\"%s\",\"kids\":\"%i\",\"distance\":\"%s\",\"colorGroup\":\"rgb(%i,%i,%i)\"}", tissue, 0, " ", colors.r, colors.g, colors.b); return; } else if (tree->left == NULL || tree->right == NULL) errAbort("\nHow did we get a node with one NULL kid??"); // Prints out the node object and opens a new children block. -//fprintf(f, "{\"%s\"%s \"%s\"%s", "name", ":", " ", ","); -fprintf(f, "{\"name\": \" \", \"kids\": \"%f\", \"colorGroup\": \"rgb(%i,%i,%i)\",",sqrt(bio->children), colors.r,colors.g,colors.b); -//fprintf(f, "\"colorGroup\": \"rgb(%i,%i,%i)\",", colors.r, colors.g, colors.b ); -distance = tree->childDistance/longest; +fprintf(f, "{\"name\": \" \", \"longestDistance\":\"%f\", \"tpmDistance\": \"%f\", \"kids\": \"%f\", \"colorGroup\": \"rgb(%i," + "%i,%i)\",",clLongest,tree->childDistance,sqrt(bio->children), colors.r,colors.g,colors.b); +distance = tree->childDistance/clLongest; if (distance != distance) distance = 0; //fprintf(f, "\"%s\"%s \"%f\"%s\n", "distance", ":", 100*distance, ","); struct rgbColor wTB; -if (distance == 0) {wTB = whiteToBlackRainbowAtPos(.95-(distance*.95));} +if (distance == 0) {wTB = whiteToBlackRainbowAtPos(.95);} else {wTB = whiteToBlackRainbowAtPos(.95-(sqrt(distance)*.95));} fprintf(f, "\"distance\": \"%f\", \"whiteToBlack\":\"rgb(%i,%i,%i)\",\n", 100*distance, wTB.r, wTB.g, wTB.b); for (i = 0; i < level + 1; i++) fputc(' ', f); fprintf(f, "\"children\":[\n"); rPrintHierarchicalJson(f, tree->left, level+1, distance); fputs(",\n", f); rPrintHierarchicalJson(f, tree->right, level+1, distance); fputc('\n', f); // Closes the children block for node objects for (i=0; i < level + 1; i++) fputc(' ', f); fputs("]\n", f); for (i = 0; i < level; i++) fputc(' ', f); @@ -444,112 +268,85 @@ assert(kid1->count == kid2->count); el->count = kid1->count; el->name = catTwoStrings(kid1->name, kid2->name); int i; for (i = 0; i < el->count; ++i) { el->vector[i] = (kid1Weight*kid1->vector[i] + kid2Weight*kid2->vector[i]); } el->children = kid1->children + kid2->children; return (struct slList *)(el); } void colorLeaves(struct slRef *leafList) /* Assign colors of rainbow to leaves. */ { -/* Loop through list once to figure out total, since we need to - * normalize */ float total = 0.0; double purplePos = 0.80; struct slRef *el, *nextEl; + +/* Loop through list once to figure out total, since we need to normalize */ for (el = leafList; el != NULL; el = nextEl) { nextEl = el->next; if (nextEl == NULL) break; struct bioExpVector *bio1 = el->val; struct bioExpVector *bio2 = nextEl->val; double distance = slBioExpVectorDistance((struct slList *)bio1, (struct slList *)bio2, NULL); if (distance != distance ) distance = 0; total += distance; } -if (total == 0) errAbort("There doesn't seem to be any difference between these matrix columns"); -/* Loop through list a second time to generate actual colors. */ + +if (total == 0) errAbort("There doesn't seem to be any difference between these matrix columns. Aborting."); + double soFar = 0; +/* Loop through list a second time to generate actual colors. */ for (el = leafList; el != NULL; el = nextEl) { nextEl = el->next; if (nextEl == NULL) break; struct bioExpVector *bio1 = el->val; struct bioExpVector *bio2 = nextEl->val; double distance = slBioExpVectorDistance((struct slList *)bio1, (struct slList *)bio2, NULL); if (distance != distance ) distance = 0 ; soFar += distance; double normalized = soFar/total; - bio2->color = saturatedRainbowAtPos(normalized*purplePos);// *purplePos + bio2->color = saturatedRainbowAtPos(normalized*purplePos); } /* Set first color to correspond to 0, since not set in above loop */ struct bioExpVector *bio = leafList->val; bio->color = saturatedRainbowAtPos(0); } - -void colorLeavesFromAttbFile(struct slRef *leafList, char *attributef, char *colorHash) -/* Assign colors of rainbow to leaves using a weird attribute file. - * And a hashing file that corresponds the group to a color. */ -{ -struct hash *hT = hashTwoColumnFile(attributef); -struct slRef *el, *nextEl; -for (el = leafList; el != NULL; el = nextEl) - { - nextEl = el->next; - if (nextEl == NULL) - break; - struct bioExpVector *bio = el->val; - struct hashEl *hEl = hashLookup(hT, bio->name); - float *something = hEl->val; - double normalized = *something / 10.0 ; - bio->color = saturatedRainbowAtPos(normalized); - } - -} - -//void verifyInput(char *expMatrix) -/* This program keeps on breaking on weird matrix column values, hopefully this - * function will weed these issues out. It will be set on by default and can be - * turned off for speed with a flag */ -//{ -//char cmd1[1024], cmd2[1024]; -//} - - void convertInput(char *expMatrix, char *descFile, bool csv) /* Takes in a expression matrix and makes the inputs that this program will use. * Namely a transposed table with the first column removed. Makes use of system calls * to use cut, sed, kent utility rowsToCols, and paste (for descFile option). */ { char cmd1[1024], cmd2[1024]; if (csv) /* A sed one liner will convert comma separated values into a tab separated values*/ { char cmd3[1024]; safef(cmd3, 1024, "sed -i 's/,/\\t/g' %s ",expMatrix); verbose(2,"%s\n", cmd3); mustSystem(cmd3); } + safef(cmd1, 1024, "cat %s | sed '1d' | rowsToCols stdin %s.transposedMatrix", expMatrix, expMatrix); /* Exp matrices are X axis of cell lines and Y axis of transcripts. This causes long Y axis and short * X axis, which are not handled well in C. The matrix is transposed to get around this issue. */ verbose(2,"%s\n", cmd1); mustSystem(cmd1); /* Pull out the cell names, and store them in a separate file. This allows the actual data matrix to * have the first row identify the transcript, then all following rows contain only expression values. * By removing the name before hand the computation was made faster and easier. */ if (descFile) { char cmd3[1024]; safef(cmd2, 1024, "rowsToCols %s stdout | cut -f1 | sed \'1d\' > %s.cellNamesTemp", expMatrix, expMatrix); safef(cmd3, 1024, "paste %s.cellNamesTemp %s > %s.cellNames", expMatrix, descFile, expMatrix); verbose(2,"%s\n", cmd2); mustSystem(cmd2); @@ -577,69 +374,74 @@ fprintf(outputFile,"ink{ fill: none; stroke: #ccc; stroke-width: 3.0px;}.selected{ fill: red;}</style><bod> <script src=\"http://d3js.org/d3.v3.min.js\" ></script> <script>var color=d3.scale.category20();var radius=%i / 2; var cluster=d3.layout.cluster().size([360, radiu",radius); fprintf(outputFile,"s - %i]); var diagonal=d3.svg.diagonal.radial().projection(function(d){return [d.y, d.x / 180 * Math.PI];}) ; var svg=d3.select(\"body\") .append(\"svg\") .attr(\"width\", radius * 2) .attr( \"height\", radius * 2) .append(\"g\") .attr(\"transform\", \"translate(\"", labelLength); fprintf(outputFile," + radius + \",\" + radius + \")\"); d3.json(\"%s\", function(error,root){ var nodes=cluster.nodes(root); var link=svg.selectAll(\"path.link\") .data(cluster.links(nodes)).enter().append(\"path\").attr(\"class\", \"link\").on(\"click\", func", jsonFile); fprintf(outputFile,"tion(){d3.select(\".selectedLink\").classed(\"selectedLink\", false) ; d3.select(this).classed(\"selectedLink\", true);}).attr(\"d\", diagonal); var node=svg.selectAll(\"g.node\") .data(nodes).enter().append(\"g\").attr(\"class\", \"node\").attr(\"transform\", function(d){return \"rotate(\" + (d.x - 90) + \")translate(\" + d.y + \")\";}).on(\"click\", function(){ d3.select(\".selected\").classed(\"selected\", false); d3.select(this).classed(\"selected\", true);}).on(\"mouseover\", function(d){ var g=d3.select(this); var info=g.ap"); fprintf(outputFile,"pend('text') .classed('info', true) .attr('x', 20) .attr('y', 10) .attr(\"transform\", function(d) {return \"rotate(\" + (90 - d.x) + \")\";}) .text(d.distance) .style(\"font-size\" ,\"15px\") .style(\"font-weight\", \"bold\");}).on(\"mouseout\", function(){ d3.select(this).select('text.info').remove();}); node.append(\"circle\") .attr(\"r\", function(d){ if (d.name==\" \"){ return d.kids;}else return 5; }).style(\"fill\", function(d){if (d.name==\" \"){return d.whiteToBlack;}else return d3.rgb(d. colorGroup);}); node.ap"); fprintf(outputFile,"pend(\"text\").attr(\"dy\", \".55em\").attr(\"text-anchor\", function(d){return d.x < 180 ? \"start\" : \"end\";}).attr(\"transform\", function (d){return d.x < 180 ? \"translate(8)\" : \"rotate(180)translate(-8)\";}).text(function(d){return d.name;});}); d3.select(self.frameElement).style(\"height\",radius * 2 + \"px\"); </script>"); carefulClose(&outputFile); } void expData(char *matrixFile, char *outDir, char *descFile) /* Read matrix and names into a list of bioExpVectors, run hacTree to * associate them, and write output. */ { +verbose(2,"Start binary clustering of the expression matrix by euclidean distance (expMatrixToJson).\n"); +clock_t begin, end; +begin = clock(); + convertInput(matrixFile, descFile, clCSV); struct bioExpVector *list = bioExpVectorListFromFile(catTwoStrings(matrixFile,".transposedMatrix")); verbose(2,"%lld allocated after bioExpVectorListFromFile\n", (long long)carefulTotalAllocated()); FILE *f = mustOpen(catTwoStrings(outDir,".json"),"w"); struct lm *localMem = lmInit(0); int size = fillInNames(list, catTwoStrings(matrixFile,".cellNames")); /* Allocate new string that is a concatenation of two strings. */ struct hacTree *clusters = NULL; + if (clMultiThreads) { - uglyf("Using %i threads. \n", clThreads); + verbose(2,"Using %i threads. \n", clThreads); clusters = hacTreeMultiThread(clThreads, (struct slList *)list, localMem, slBioExpVectorDistance, slBioExpVectorMerge, NULL, NULL); } else { - uglyf("Using 1 threads. \n"); + verbose(2,"Using 1 threads. \n"); clusters = hacTreeFromItems((struct slList *)list, localMem, slBioExpVectorDistance, slBioExpVectorMerge, NULL, NULL); } + struct slRef *orderedList = getOrderedLeafList(clusters); colorLeaves(orderedList); -if (clForceLayout) - printForceLayoutJson(f,clusters); -else{ printHierarchicalJson(f, clusters); FILE *htmlF = mustOpen(catTwoStrings(outDir,".html"),"w"); generateHtml(htmlF,size,catTwoStrings(outDir,".json")); - } + // Remove temporary files char cleanup[1024], cleanup2[1024]; safef(cleanup, 1024, "rm %s.cellNames", matrixFile); safef(cleanup2, 1024, "rm %s.transposedMatrix", matrixFile); mustSystem(cleanup); mustSystem(cleanup2); -verbose(2,"%lld allocated at end\n", (long long)carefulTotalAllocated()); +end = clock(); +verbose(2,"%lld allocated at end. The program took %f seconds to complete.\n", (long long)carefulTotalAllocated(), (double)(end-begin)/CLOCKS_PER_SEC); + +verbose(2,"Completed binary clustering of the expression matrix by euclidean distance (expMatrixToJson).\n"); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); -clForceLayout = optionExists("forceLayout"); clCSV = optionExists("CSV"); clMultiThreads = optionExists("multiThreads"); clThreads = optionInt("threads", clThreads); clMemLim = optionInt("memLim", clMemLim); clDescFile = optionVal("descFile", clDescFile); if (argc != 3) usage(); pushCarefulMemHandler(1L*1024*1024*1024*clMemLim); expData(argv[1], argv[2], clDescFile); return 0; }