void makeTmpSai(struct sqlConnection *conn, struct cdwValidFile *vf, char *genoFile,
char **retSampleFile, char **retSaiFile)
/* Given a fastq file, make a subsample of it 100k reads long and align it with
* bwa producing a sai file of given name. */
{
/* Get fastq record */
long long fileId = vf->fileId;
struct cdwFastqFile *fqf = cdwFastqFileFromFileId(conn, fileId);
if (fqf == NULL)
errAbort("No cdwFastqFile record for file id %lld", fileId);
/* Create downsampled fastq in temp directory - downsampled more than default even. */
char sampleFastqName[PATH_LEN];
cdwMakeTempFastqSample(fqf->sampleFileName, FASTQ_SAMPLE_SIZE, sampleFastqName);
verbose(1, "downsampled %s into %s\n", vf->licensePlate, sampleFastqName);
/* Do alignment */
char cmd[3*PATH_LEN];
char *saiName = cloneString(rTempName(cdwTempDir(), "cdwPairSample", ".sai"));
safef(cmd, sizeof(cmd), "bwa aln -t 3 %s %s > %s", genoFile, sampleFastqName, saiName);
mustSystem(cmd);
/* Save return variables, clean up, and go home. */
*retSampleFile = cloneString(sampleFastqName);
*retSaiFile = saiName;
cdwFastqFileFree(&fqf);
}
void fastqRepeatQa(struct sqlConnection *conn, struct cdwFile *ef, struct cdwValidFile *vf)
/* Do repeat QA if possible on fastq file. */
{
/* First see if total repeat content is already in our table, in which case we are done. */
long long fileId = ef->id;
char query[512];
sqlSafef(query, sizeof(query),
"select count(*) from cdwQaRepeat where fileId=%lld and repeatClass='total'" , fileId);
if (sqlQuickNum(conn, query) != 0)
return; /* We've done this already */
/* Get sample file name from fastq table. */
struct cdwFastqFile *fqf = cdwFastqFileForFileId(conn, fileId);
if (fqf == NULL)
errAbort("No edqFastqRecord for %s", vf->licensePlate);
char *fastqPath = fqf->sampleFileName;
char bwaIndex[PATH_LEN];
safef(bwaIndex, sizeof(bwaIndex), "%s%s/repeatMasker/repeatMasker.fa",
cdwValDataDir, vf->ucscDb);
char cmd[3*PATH_LEN];
char *saiName = cloneString(rTempName(cdwTempDir(), "cdwQaRepeat", ".sai"));
safef(cmd, sizeof(cmd), "bwa aln %s %s > %s", bwaIndex, fastqPath, saiName);
mustSystem(cmd);
char *samName = cloneString(rTempName(cdwTempDir(), "cdwQaRepeat", ".sam"));
safef(cmd, sizeof(cmd), "bwa samse %s %s %s > %s", bwaIndex, saiName, fastqPath, samName);
mustSystem(cmd);
remove(saiName);
char *raName = cloneString(rTempName(cdwTempDir(), "cdwQaRepeat", ".ra"));
safef(cmd, sizeof(cmd), "edwSamRepeatAnalysis %s %s", samName, raName);
mustSystem(cmd);
verbose(2, "mustSystem(%s)\n", cmd);
remove(samName);
raIntoCdwRepeatQa(raName, conn, fileId);
remove(raName);
#ifdef SOON
#endif /* SOON */
freez(&saiName);
freez(&samName);
freez(&raName);
cdwFastqFileFree(&fqf);
}
