int main(int argc, char **argv)
{
AjPFile outfile = NULL;
AjBool full = AJFALSE;
AjPStr tmpstr = NULL;
embInit("embossversion", argc, argv);
full = ajAcdGetBoolean("full");
outfile = ajAcdGetOutfile("outfile");
if (!full) {
ajFmtPrintF(outfile,"%s\n", VERSION);
}
else {
tmpstr = ajStrNewRes(128);
ajStrAssignS(&tmpstr, ajNamValuePackage());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "PackageName: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueVersion());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "LibraryVersion: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueSystem());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "System: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueInstalldir());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "InstallDirectory: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueRootdir());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "RootDirectory: %S\n", tmpstr);
ajStrAssignS(&tmpstr, ajNamValueBasedir());
if (!ajStrGetLen(tmpstr))
ajStrAssignC(&tmpstr, "(unknown)");
ajFmtPrintF(outfile, "BaseDirectory: %S\n", tmpstr);
if (!ajNamGetValueC("acdroot", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_AcdRoot: %S\n", tmpstr);
if (!ajNamGetValueC("data", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Data: %S\n", tmpstr);
if (!ajNamGetValueC("filter", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Filter: %S\n", tmpstr);
if (!ajNamGetValueC("format", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Format: %S\n", tmpstr);
if (!ajNamGetValueC("graphics", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Graphics: %S\n", tmpstr);
if (!ajNamGetValueC("httpversion", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_HttpVersion: %S\n", tmpstr);
if (!ajNamGetValueC("language", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Language: %S\n", tmpstr);
if (!ajNamGetValueC("options", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Options: %S\n", tmpstr);
if (!ajNamGetValueC("outdirectory", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_OutDirectory: %S\n", tmpstr);
if (!ajNamGetValueC("outfeatformat", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_OutFeatFormat: %S\n", tmpstr);
if (!ajNamGetValueC("outformat", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_OutFormat: %S\n", tmpstr);
if (!ajNamGetValueC("proxy", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Proxy: %S\n", tmpstr);
if (!ajNamGetValueC("stdout", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_Stdout: %S\n", tmpstr);
if (!ajNamGetValueC("warnrange", &tmpstr))
ajStrAssignC(&tmpstr, "(default)");
ajFmtPrintF(outfile, "Emboss_WarnRange: %S\n", tmpstr);
}
ajFileClose(&outfile);
embExit();
return 0;
}
static AjBool assemoutWriteNextSam(AjPOutfile outfile, const AjPAssem assem)
{
AjPFile outf = ajOutfileGetFile(outfile);
AjPAssemContig c = NULL;
AjPAssemRead r = NULL;
AjPAssemTag t = NULL;
AjPAssemContig* contigs = NULL;
AjIList j = NULL;
AjPStr argstr = NULL;
const AjPStr headertext = NULL;
ajint n = 0;
ajulong i = 0UL;
AjBool ret = ajTrue;
if(!outf || !assem)
return ajFalse;
ajDebug("assemoutWriteSam: # of contigs = %d\n", n);
if(!assem->Hasdata)
{
ajFmtPrintF(outf, "@HD\tVN:1.3\tSO:%s\n", ajAssemGetSortorderC(assem));
/* Program record */
argstr = ajStrNewS(ajUtilGetCmdline());
ajStrExchangeKK(&argstr, '\n', ' ');
ajFmtPrintF(outf, "@PG\tID:%S\tVN:%S\tCL:%S\n",
ajUtilGetProgram(), ajNamValueVersion(), argstr);
ajStrDel(&argstr);
if(ajListGetLength(assem->ContigsOrder))
ajListToarray(assem->ContigsOrder, (void***)&contigs);
else
ajTableToarrayValues(assem->Contigs, (void***)&contigs);
while (contigs[i]) /* contigs */
{
c = contigs[i++];
if(!ajStrMatchC(c->Name, "*"))
{
ajFmtPrintF(outf, "@SQ\tSN:%S\tLN:%d", c->Name, c->Length);
if(c->URI)
ajFmtPrintF(outf, "\tUR:%S", c->URI);
if(c->MD5)
ajFmtPrintF(outf, "\tM5:%S", c->MD5);
if(c->Species)
ajFmtPrintF(outf, "\tSP:%S", c->Species);
ajFmtPrintF(outf, "\n");
j = ajListIterNewread(c->Tags);
while (!ajListIterDone(j))
{
t = ajListIterGet(j);
ajFmtPrintF(outf, "@CO\t%S %u %u %S\n",
t->Name, t->x1, t->y1,
t->Comment);
}
ajListIterDel(&j);
}
}
headertext = assemSAMGetReadgroupHeaderlines(assem);
if(headertext)
ajFmtPrintF(outf,"%S", headertext);
AJFREE(contigs);
if(!assem->BamHeader)
return ajTrue;
}
/* data */
j = ajListIterNewread(assem->Reads);
if(ajListGetLength(assem->ContigsOrder))
i = ajListToarray(assem->ContigsOrder, (void***)&contigs);
else
i = ajTableToarrayValues(assem->Contigs, (void***)&contigs);
while (!ajListIterDone(j)) /* reads */
{
r = ajListIterGet(j);
assemoutWriteSamAlignment(outf, r, contigs, (ajuint) i);
}
ajListIterDel(&j);
AJFREE(contigs);
return ret;
}
