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cmd_cram_dsc_dump2pileup.cpp
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cmd_cram_dsc_dump2pileup.cpp
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#include "cramore.h"
#include "sc_drop_seq.h"
#include "genomeLoci.h"
#include <sys/stat.h>
// TODO : Record strand info
// TODO : Reduce memory footprint
int32_t cmdCramDscDump2Pileup(int32_t argc, char** argv) {
std::string inPrefix;
std::string outPrefix;
int32_t chunk_id = -1;
paramList pl;
BEGIN_LONG_PARAMS(longParameters)
LONG_PARAM_GROUP("Required pptions for input/output files", NULL)
LONG_STRING_PARAM("in",&inPrefix, "Input prefix from cramore/popscle dsc-dump")
LONG_STRING_PARAM("out",&outPrefix, "Output prefix compatible with cramore/popscle dsc-pileup")
LONG_PARAM_GROUP("Additional options for input files", NULL)
LONG_INT_PARAM("chunk-id",&chunk_id, "Chunk ID to focus on. By default, it runs across all chunks")
END_LONG_PARAMS();
pl.Add(new longParams("Available Options", longParameters));
pl.Read(argc, argv);
pl.Status();
if ( inPrefix.empty() )
error("Missing required option --in-prefix");
notice("Reading %s.barcodes.tsv.gz", inPrefix.c_str());
// read the input barcodes and variants first
tsv_reader tsv_bcds( (inPrefix + ".barcodes.tsv.gz").c_str() );
tsv_bcds.read_line(); // skip the first line
std::vector<std::string> bcds;
std::vector< std::vector<int> > ibcd2chunks;
while( tsv_bcds.read_line() > 0 ) {
if ( tsv_bcds.nfields != 3 )
error("Cannot parse the line %s because it does not have 3 tokens as expected", tsv_bcds.str.s);
if ( tsv_bcds.int_field_at(0) != (int32_t)bcds.size() )
error("Cannot parse the line %s because expected ID is %d but observed is %d", (int32_t)bcds.size(), tsv_bcds.int_field_at(0));
if ( ibcd2chunks.size() <= tsv_bcds.int_field_at(2) )
ibcd2chunks.resize(tsv_bcds.int_field_at(2)+1);
ibcd2chunks[tsv_bcds.int_field_at(2)].push_back(tsv_bcds.int_field_at(0));
bcds.push_back(tsv_bcds.str_field_at(1));
}
tsv_reader tsv_vars;
std::map<std::string,int32_t> chrom2rid;
std::vector<std::string> chroms;
std::vector<int32_t> rids;
std::vector<int32_t> poss;
std::vector<std::string> refs;
std::vector<std::string> alts;
std::vector<double> afs;
bool skipVars = false;
notice("Reading %s.variants.tsv.gz", inPrefix.c_str());
if ( tsv_vars.open( (inPrefix + ".variants.tsv.gz").c_str() ) ) {
htsFile* wV = hts_open((outPrefix+".var.gz").c_str(),"wg");
hprintf(wV, "#SNP_ID\tCHROM\tPOS\tREF\tALT\tAF\n");
tsv_vars.read_line();
while( tsv_vars.read_line() > 0 ) {
if ( tsv_vars.int_field_at(0) != rids.size() )
error("Cannot parse the line because expected ID is %d but observed is %d", (int32_t)rids.size(), tsv_vars.int_field_at(0));
std::string chr = tsv_vars.str_field_at(1);
if ( chrom2rid.find(chr) == chrom2rid.end() ) {
chrom2rid[chr] = chroms.size();
chroms.push_back(chr);
}
rids.push_back(chrom2rid[chr]);
poss.push_back(tsv_vars.int_field_at(2));
refs.push_back(tsv_vars.str_field_at(3));
alts.push_back(tsv_vars.str_field_at(4));
afs.push_back(tsv_vars.double_field_at(5));
//error("%d %s %s %.5lf",tsv_vars.int_field_at(2),tsv_vars.str_field_at(3),tsv_vars.str_field_at(4),tsv_vars.double_field_at(5));
hprintf(wV, "%d\t%s\t%d\t%c\t%c\t%.5lf\n", (int32_t)rids.size()-1, chr.c_str(), poss.back(), refs.back()[0], alts.back()[0], afs.back());
}
hts_close(wV);
}
else {
notice("No variant file found at %s.variants.tsv.gz. Skipping reading..", inPrefix.c_str());
skipVars = true;
}
// process each chunk separately
int32_t bcdOffset = 0;
char buf[65535];
htsFile* wC = hts_open((outPrefix+".cel.gz").c_str(),"wg");
htsFile* wP = skipVars ? NULL : hts_open((outPrefix+".plp.gz").c_str(),"wg");
htsFile* wU = hts_open((outPrefix+".umi.gz").c_str(),"wg");
hprintf(wC, "#DROPLET_ID\tBARCODE\tNUM.READ\tNUM.UMI\tNUM.UMIwSNP\tNUM.SNP\n");
if ( !skipVars )
hprintf(wP, "#DROPLET_ID\tSNP_ID\tALLELES\tBASEQS\n");
for(int32_t i=0; i < (int32_t)ibcd2chunks.size(); ++i) {
notice("Processing chunk %d..",i);
sc_dropseq_lib_t* pscl = new sc_dropseq_lib_t; // for pileup info
for(int32_t j=0; j < (int32_t)rids.size(); ++j) {
pscl->add_snp(rids[j], poss[j], refs[j][0], alts[j][0], afs[j], NULL);
}
std::map<int32_t,int32_t> ibcd_map;
for(int32_t j=0; j < (int32_t)ibcd2chunks[i].size(); ++j) {
int32_t ibcd = pscl->add_cell(bcds[ibcd2chunks[i][j]].c_str());
if ( ibcd != j )
error("Unexpected barcode ID %d when expecting %d", ibcd, j);
ibcd_map[ibcd2chunks[i][j]] = ibcd;
}
std::vector<std::map<std::string, std::pair<genomeLoci,genomeLoci>> > umiLoci(ibcd2chunks[i].size()); // fwd/rev pair
sprintf(buf, "%s.tmp/chunk.%05d.tsv.gz", inPrefix.c_str(), i);
tsv_reader tsv_chunk(buf);
while(tsv_chunk.read_line() > 0) {
int ic = tsv_chunk.int_field_at(0);
//notice("ic = %d",ic);
std::map<int32_t,int32_t>::iterator it = ibcd_map.find(ic);
if ( it == ibcd_map.end() )
error("Cannot find %d from ibcd_map", ic);
int ib = it->second;
std::string sumi = tsv_chunk.str_field_at(1);
bool revStrand = tsv_chunk.str_field_at(2)[0] == '-';
int nloci = tsv_chunk.int_field_at(3);
int nvars = tsv_chunk.int_field_at(4);
if ( nloci > 0 ) {
genomeLoci& loci = revStrand ? umiLoci[ib][sumi].second : umiLoci[ib][sumi].first;
for(int32_t j=0; j < nloci; ++j) {
const char* s1 = tsv_chunk.str_field_at(5+j);
const char* s2 = strchr(s1,':')+1;
const char* s3 = strchr(s2,':')+1;
std::string s1_str(s1,s2-s1-1);
int32_t s2_int = atoi(s2);
int32_t s3_int = atoi(s3);
loci.add(s1_str.c_str(), s2_int, s3_int);
}
loci.resolveOverlaps();
}
if ( nvars > 0 ) {
for(int32_t j=0; j < nvars; ++j) {
const char* s1 = tsv_chunk.str_field_at(5+nloci+j);
const char* s2 = strchr(s1,':')+1;
const char* s3 = strchr(s2,':')+1;
int32_t s1_int = atoi(s1);
int32_t s2_int = atoi(s2);
int32_t s3_int = atoi(s3);
pscl->add_read(s1_int, ib, sumi.c_str(), s2_int, s3_int);
}
}
++(pscl->cell_totl_reads[ib]);
}
// write cell barcodes
for(int32_t j=0; j < (int32_t)ibcd2chunks[i].size(); ++j) {
hprintf(wC, "%d\t%s\t%d\t%u\t%d\t%u\n", j + bcdOffset, bcds[ibcd2chunks[i][j]].c_str(), pscl->cell_totl_reads[j], umiLoci[j].size(), pscl->cell_uniq_reads[j], pscl->cell_umis[j].size());
}
// write UMIs
for(int32_t j=0; j < (int32_t)umiLoci.size(); ++j) {
for(std::map<std::string, std::pair<genomeLoci,genomeLoci> >::iterator itu = umiLoci[j].begin();
itu != umiLoci[j].end(); ++itu) {
if ( !( itu->second.first.empty() && itu->second.second.empty() ) ) { // at least fwd or rev is not empty
hprintf(wU, "%d\t%s\t%u\t%u", j + bcdOffset, itu->first.c_str(), itu->second.first.totalLength(), itu->second.second.totalLength());
for(itu->second.first.rewind(); !itu->second.first.isend(); itu->second.first.next()) {
hprintf(wU, "\t%s:%d:%d:+", itu->second.first.it->chrom.c_str(), itu->second.first.it->beg1, itu->second.first.it->end0 - itu->second.first.it->beg1 + 1);
}
for(itu->second.second.rewind(); !itu->second.second.isend(); itu->second.second.next()) {
hprintf(wU, "\t%s:%d:%d:-", itu->second.second.it->chrom.c_str(), itu->second.second.it->beg1, itu->second.second.it->end0 - itu->second.second.it->beg1 + 1);
}
hprintf(wU, "\n");
}
}
}
// write pileups
if ( !skipVars ) {
for(int32_t j=0; j < pscl->nsnps; ++j) {
std::map<int32_t,sc_snp_droplet_t*>& cells = pscl->snp_umis[j];
if ( cells.empty() ) continue;
std::map<int32_t,sc_snp_droplet_t*>::iterator it;
for(it = cells.begin(); it != cells.end(); ++it) {
std::string s_als;
std::string s_bqs;
for(sc_snp_droplet_it_t it2=it->second->begin(); it2 != it->second->end(); ++it2) {
uint8_t al = ( it2->second >> 24 ) & 0x00ff;
uint8_t bq = ( it2->second >> 16 ) & 0x00ff;
s_als += ('0' + al);
s_bqs += (33 + bq);
}
hprintf(wP, "%d\t%d\t%s\t%s\n", it->first + bcdOffset, j, s_als.c_str(), s_bqs.c_str());
}
}
}
bcdOffset += (int32_t)ibcd2chunks[i].size();
umiLoci.clear();
delete pscl;
}
if ( !skipVars ) hts_close(wP);
hts_close(wC);
hts_close(wU);
notice("Analysis finished");
return 0;
}