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Remove obsolete HTML output.
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@brianwalenz
brianwalenz committed Sep 16, 2016
1 parent 216b39c commit 28f56f5
Showing 1 changed file with 0 additions and 96 deletions.
96 changes: 0 additions & 96 deletions src/stores/gatekeeperCreate.C
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Original file line number Diff line number Diff line change
Expand Up @@ -359,17 +359,6 @@ loadReads(gkStore *gkpStore,
fprintf(stderr, "\n");
fprintf(stderr, " Loading reads from '%s'\n", fileName);

#if 0
fprintf(htmlLog, "<tr id='gkpload%u'><td colspan='2'>%s</td></tr>\n", gkpFileID, fileName);
fprintf(htmlLog, "<tr class='details'><td rowspan='9'>Parameters</td><td>preset=N/A</td></tr>\n");
fprintf(htmlLog, "<tr class='details'><td>defaultQV=%u</td></tr>\n", gkpLibrary->gkLibrary_defaultQV());
fprintf(htmlLog, "<tr class='details'><td>isNonRandom=%s</td></tr>\n", gkpLibrary->gkLibrary_isNonRandom() ? "true" : "false");
fprintf(htmlLog, "<tr class='details'><td>removeDuplicateReads=%s</td></tr>\n", gkpLibrary->gkLibrary_removeDuplicateReads() ? "true" : "false");
fprintf(htmlLog, "<tr class='details'><td>finalTrim=%s</td></tr>\n", gkpLibrary->gkLibrary_finalTrim() ? "true" : "false");
fprintf(htmlLog, "<tr class='details'><td>removeSpurReads=%s</td></tr>\n", gkpLibrary->gkLibrary_removeSpurReads() ? "true" : "false");
fprintf(htmlLog, "<tr class='details'><td>removeChimericReads=%s</td></tr>\n", gkpLibrary->gkLibrary_removeChimericReads() ? "true" : "false");
fprintf(htmlLog, "<tr class='details'><td>checkForSubReads=%s</td></tr>\n", gkpLibrary->gkLibrary_checkForSubReads() ? "true" : "false");
#else
fprintf(htmlLog, "nam "F_U32" %s\n", gkpFileID, fileName);

fprintf(htmlLog, "lib preset=N/A");
Expand All @@ -380,8 +369,6 @@ loadReads(gkStore *gkpStore,
fprintf(htmlLog, " removeSpurReads=%s", gkpLibrary->gkLibrary_removeSpurReads() ? "true" : "false");
fprintf(htmlLog, " removeChimericReads=%s", gkpLibrary->gkLibrary_removeChimericReads() ? "true" : "false");
fprintf(htmlLog, " checkForSubReads=%s\n", gkpLibrary->gkLibrary_checkForSubReads() ? "true" : "false");
#endif


compressedFileReader *F = new compressedFileReader(fileName);

Expand Down Expand Up @@ -513,25 +500,12 @@ loadReads(gkStore *gkpStore,

// Write status to HTML

#if 0
fprintf(htmlLog, "<tr class='details'><td rowspan='2'>FASTA</td><td>"F_U32" reads ("F_U64" bp)</td></tr>\n", nLOADEDAlocal, bLOADEDAlocal);
fprintf(htmlLog, "<tr class='details'><td>"F_U32" reads ("F_U64" bp) were short and not loaded</td></tr>\n", nSKIPPEDAlocal, bSKIPPEDAlocal);

fprintf(htmlLog, "<tr class='details'><td rowspan='2'>FASTQ</td><td>"F_U32" reads ("F_U64" bp)</td></tr>\n", nLOADEDQlocal, bLOADEDQlocal);
fprintf(htmlLog, "<tr class='details'><td>"F_U32" reads ("F_U64" bp) were short and not loaded</td></tr>\n", nSKIPPEDQlocal, bSKIPPEDQlocal);

fprintf(htmlLog, "<tr><td colspan='2'>"F_U32" reads ("F_U64" bp) loaded, "F_U32" reads ("F_U64" bp) skipped, "F_U32" warnings</td></tr>\n",
nLOADEDAlocal + nLOADEDQlocal, bLOADEDAlocal + bLOADEDQlocal,
nSKIPPEDAlocal + nSKIPPEDQlocal, bSKIPPEDAlocal + bSKIPPEDQlocal,
nWARNSlocal);
#else
fprintf(htmlLog, "dat "F_U32" "F_U64" "F_U32" "F_U64" "F_U32" "F_U64" "F_U32" "F_U64" "F_U32"\n",
nLOADEDAlocal, bLOADEDAlocal,
nSKIPPEDAlocal, bSKIPPEDAlocal,
nLOADEDQlocal, bLOADEDQlocal,
nSKIPPEDQlocal, bSKIPPEDQlocal,
nWARNSlocal);
#endif

// Add the just loaded numbers to the global numbers

Expand Down Expand Up @@ -645,26 +619,6 @@ main(int argc, char **argv) {
uint32 nSKIPPED = 0;
uint64 bSKIPPED = 0; // Bases not loaded, too short

#if 0
fprintf(htmlLog, "<!DOCTYPE html>\n");
fprintf(htmlLog, "<html>\n");
fprintf(htmlLog, "<head>\n");
fprintf(htmlLog, "<title>gatekeeper load statistics</title>\n");
fprintf(htmlLog, "<style type='text/css'>\n");
fprintf(htmlLog, "body { font-family: Helvetica, Verdana, sans-serif; }\n");
fprintf(htmlLog, "h1, h2 { color: #ee3e80; }\n");
fprintf(htmlLog, "p { color: #665544; }\n");
fprintf(htmlLog, "th, td { border: 1px solid #111111; padding: 2px 2px 2px 2px; }\n");
fprintf(htmlLog, "td:hover { background-color: #e4e4e4; }\n");
fprintf(htmlLog, "th:hover { background-color: #d4d4d4; }\n");
fprintf(htmlLog, "tr.details { visibility: collapse; }\n");
fprintf(htmlLog, "</style>\n");
fprintf(htmlLog, "</head>\n");
fprintf(htmlLog, "<body>\n");
fprintf(htmlLog, "<h2>Input Files</h2>\n");
fprintf(htmlLog, "<table>\n");
#endif

for (; firstFileArg < argc; firstFileArg++) {
fprintf(stderr, "\n");
fprintf(stderr, "Starting file '%s'.\n", argv[firstFileArg]);
Expand Down Expand Up @@ -745,10 +699,6 @@ main(int argc, char **argv) {
delete [] linekv;
}

#if 0
fprintf(htmlLog, "</table>\n");
#endif

gkpStore->gkStore_close();

fclose(nameMap);
Expand All @@ -758,12 +708,6 @@ main(int argc, char **argv) {
fprintf(stderr, "Finished with:\n");
fprintf(stderr, " "F_U32" warnings (bad base or qv, too short, too long)\n", nWARNS);
fprintf(stderr, "\n");
#if 0
fprintf(stderr, "Read from inputs:\n");
fprintf(stderr, " "F_U64" bp.\n", bLOADED);
fprintf(stderr, " "F_U32" reads.\n", nLOADED);
fprintf(stderr, "\n");
#endif
fprintf(stderr, "Loaded into store:\n");
fprintf(stderr, " "F_U64" bp.\n", bLOADED);
fprintf(stderr, " "F_U32" reads.\n", nLOADED);
Expand All @@ -773,50 +717,10 @@ main(int argc, char **argv) {
fprintf(stderr, " "F_U32" reads (%.4f%%).\n", nSKIPPED, 100.0 * nSKIPPED / (nSKIPPED + nLOADED));
fprintf(stderr, "\n");
fprintf(stderr, "\n");

#if 0
fprintf(htmlLog, "\n");
fprintf(htmlLog, "<h2>Final Store</h2>\n");
fprintf(htmlLog, "<table>\n");
fprintf(htmlLog, "<tr><td colspan='2'>%s</td></tr>\n", gkpStoreName);
fprintf(htmlLog, "<tr><td>readsLoaded</td><td>"F_U32" reads ("F_U64" bp)</td></tr>\n", nLOADED, bLOADED);
fprintf(htmlLog, "<tr><td>readsSkipped</td><td>"F_U32" reads ("F_U64" bp) (read was too short)</td></tr>\n", nSKIPPED, bSKIPPED);
fprintf(htmlLog, "<tr><td>warnings</td><td>"F_U32" warnings (invalid base or quality value)</td></tr>\n", nWARNS);
fprintf(htmlLog, "</table>\n");
fprintf(htmlLog, "\n");

fprintf(htmlLog, "<script type='text/javascript'>\n");
fprintf(htmlLog, "var toggleOne = function() {\n");
fprintf(htmlLog, " var table = this.closest('table');\n");
fprintf(htmlLog, " var elts = table.querySelectorAll('.details');\n");
fprintf(htmlLog, "\n");
fprintf(htmlLog, " for (var i=0; i<elts.length; i++) {\n");
fprintf(htmlLog, " if (!elts[i].enabled) {\n");
fprintf(htmlLog, " elts[i].enabled = true;\n");
fprintf(htmlLog, " elts[i].style.visibility = 'visible';\n");
fprintf(htmlLog, " } else {\n");
fprintf(htmlLog, " elts[i].enabled = false;\n");
fprintf(htmlLog, " elts[i].style.visibility = 'collapse';\n");
fprintf(htmlLog, " }\n");
fprintf(htmlLog, " }\n");
fprintf(htmlLog, "}\n");
fprintf(htmlLog, "\n");
for (uint32 ii=0; ii<gkpFileID; ii++) {
fprintf(htmlLog, "document.getElementById('gkpload%u').onclick = toggleOne;\n", ii);
fprintf(htmlLog, "document.getElementById('gkpload%u').style = 'cursor: pointer;';\n", ii);
}
fprintf(htmlLog, "</script>\n");
fprintf(htmlLog, "\n");
fprintf(htmlLog, "</body>\n");
fprintf(htmlLog, "</html>\n");
#else
fprintf(htmlLog, "sum "F_U32" "F_U64" "F_U32" "F_U64" "F_U32"\n", nLOADED, bLOADED, nSKIPPED, bSKIPPED, nWARNS);
#endif

fclose(htmlLog);



if (nERROR > 0)
fprintf(stderr, "gatekeeperCreate did NOT finish successfully; too many errors.\n");

Expand Down

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