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command line parse fix
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Jeremiah Wala committed Aug 27, 2016
1 parent 8c7239b commit 20aa24a
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Showing 6 changed files with 31 additions and 39 deletions.
2 changes: 1 addition & 1 deletion SeqLib
Submodule SeqLib updated from 0e3cee to b0da25
22 changes: 10 additions & 12 deletions src/CommandLineRegion.h
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Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,9 @@ CommandLineRegion(const std::string& mf, int t) : f(mf), type(t), pad(0), i_flag

};

static SeqLib::ReadFilter BuildReadFilterFromCommandLineRegion(const CommandLineRegion& c, const SeqLib::BamHeader& hdr) {
static SeqLib::Filter::ReadFilter BuildReadFilterFromCommandLineRegion(const CommandLineRegion& c, const SeqLib::BamHeader& hdr) {

SeqLib::ReadFilter r;
SeqLib::Filter::ReadFilter r;
//r.m_region_file = c.f;

// set a whole genome ALL rule
Expand All @@ -48,7 +48,7 @@ static SeqLib::ReadFilter BuildReadFilterFromCommandLineRegion(const CommandLine
}

// add the abstract rule
SeqLib::AbstractRule ar;
SeqLib::Filter::AbstractRule ar;

// set the flag
if (c.i_flag || c.e_flag) {
Expand All @@ -58,28 +58,26 @@ static SeqLib::ReadFilter BuildReadFilterFromCommandLineRegion(const CommandLine

// set the other fields
if (c.len)
ar.len = SeqLib::Range(c.len, INT_MAX, false);
ar.len = SeqLib::Filter::Range(c.len, INT_MAX, false);
if (c.nbases != INT_MAX)
ar.nbases = SeqLib::Range(0, c.nbases, false);
ar.nbases = SeqLib::Filter::Range(0, c.nbases, false);
if (c.phred)
ar.phred = SeqLib::Range(c.phred, INT_MAX, false);
ar.phred = SeqLib::Filter::Range(c.phred, INT_MAX, false);
if (c.mapq)
ar.mapq = SeqLib::Range(c.mapq, INT_MAX, false);
ar.mapq = SeqLib::Filter::Range(c.mapq, INT_MAX, false);
if (c.clip)
ar.clip = SeqLib::Range(c.clip, INT_MAX, false);
ar.clip = SeqLib::Filter::Range(c.clip, INT_MAX, false);
if (c.del)
ar.del = SeqLib::Range(c.del, INT_MAX, false);
ar.del = SeqLib::Filter::Range(c.del, INT_MAX, false);
if (c.ins)
ar.ins = SeqLib::Range(c.ins, INT_MAX, false);
ar.ins = SeqLib::Filter::Range(c.ins, INT_MAX, false);

// set the id
//ar.id = id + "_CMD_RULE";

#ifdef HAVE_AHO_CORASICK
// add a motif rule
if (!c.motif.empty())
ar.addMotifRule(c.motif, false);
#endif

// add read group rule
ar.SetReadGroup(c.rg);
Expand Down
4 changes: 2 additions & 2 deletions src/STCoverage.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,12 @@

void STCoverage::settleCoverage() {
SeqLib::GRC tmp = m_grc;
m_grc.mergeOverlappingIntervals();
m_grc.MergeOverlappingIntervals();
}

STCoverage::STCoverage(const SeqLib::GenomicRegion& gr) {
m_gr = gr;
v = uint16_sp(new std::vector<uint16_t>(gr.width(),0));
v = uint16_sp(new std::vector<uint16_t>(gr.Width(),0));
}

uint16_t STCoverage::maxCov() const {
Expand Down
14 changes: 5 additions & 9 deletions src/VariantBamWalker.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ void VariantBamWalker::writeVariantBam()
SeqLib::BamRecordVector buffer;

// check if the BAM is sorted by looking at the header
std::string hh = m_hdr.AsString(); //std::string(header()->text);
std::string hh = Header().AsString(); //std::string(header()->text);
bool sorted = hh.find("SO:coord") != std::string::npos;

if (!sorted && max_cov > 0) {
Expand All @@ -27,8 +27,8 @@ void VariantBamWalker::writeVariantBam()

// check that regions are sufficient size
for (auto& k : m_region)
if (k.width() < 1000)
k.pad(1000);
if (k.Width() < 1000)
k.Pad(1000);

while (GetNextRecord(r)) {

Expand All @@ -37,7 +37,6 @@ void VariantBamWalker::writeVariantBam()
// prepare for case of long reads
buffer_size = std::max((int32_t)r.Length() * 5, buffer_size);

//std::cerr << "...r " << r << " rule " << rule << std::endl;
TrackSeenRead(r);

// add coverage
Expand Down Expand Up @@ -160,15 +159,12 @@ void VariantBamWalker::printMessage(const SeqLib::BamRecord &r) const

if (rc_main.total <= 0) {
std::sprintf(buffer, "NO READS FOUND at %2s:%-11s",chrname.c_str(), posstring.c_str());
std::string outr(buffer);
//std::cerr << outr << SnowTools::displayRuntime(start) << std::endl;
std::cerr << std::string(buffer) << std::endl;
return;
}

std::sprintf (buffer, "Read %11s at %2s:%-11s. Kept %10s (%2d%%) -- ",
rc_main.totalString().c_str(), chrname.c_str(), posstring.c_str(),
rc_main.keepString().c_str(), rc_main.percent());
std::string outr(buffer);
//std::cerr << outr << SnowTools::displayRuntime(start) << std::endl;;

std::cerr << std::string(buffer) << std::endl;
}
6 changes: 2 additions & 4 deletions src/VariantBamWalker.h
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,7 @@ class VariantBamWalker: public SeqLib::BamReader
{
public:

VariantBamWalker() {}

VariantBamWalker(const std::string in) : SeqLib::BamReader(in) {}
VariantBamWalker() {}

void writeVariantBam();

Expand All @@ -37,7 +35,7 @@ class VariantBamWalker: public SeqLib::BamReader

bool m_verbose = false;

SeqLib::ReadFilterCollection m_mr;
SeqLib::Filter::ReadFilterCollection m_mr;

SeqLib::BamWriter m_writer;

Expand Down
22 changes: 11 additions & 11 deletions src/variant.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -36,10 +36,10 @@ static const char *VARIANT_BAM_USAGE_MESSAGE =
" Description: Filter a BAM/SAM/CRAM/STDIN according to hierarchical rules\n"
"\n"
" General options\n"
" --help Display this help and exit\n"
" -h, --help Display this help and exit\n"
" -v, --verbose Verbose output\n"
//" -c, --counts-file File to place read counts per rule / region\n"
" -x, --no-output Don't output reads (used for profiling with -q and/or counting with -c)\n"
" -x, --no-output Don't output reads (used for profiling with -q)\n"
" -r, --rules JSON ecript for the rules.\n"
" -k, --proc-regions-file Samtools-style region string (e.g. 1:1,000-2,000) or BED of regions to process\n"
" Output options\n"
Expand All @@ -63,9 +63,9 @@ static const char *VARIANT_BAM_USAGE_MESSAGE =
" --min-clip Minimum number of quality clipped bases\n"
" --max-nbases Maximum number of N bases\n"
" --min-mapq Minimum mapping quality\n"
" --min-del Minimum number of inserted bases\n"
" --min-ins Minimum number of deleted bases\n"
" --min-readlength Minimum read length (after base-quality trimming)\n"
" --min-del Minimum number of deleted bases\n"
" --min-ins Minimum number of inserted bases\n"
" --min-length Minimum read length (after base-quality trimming)\n"
" --motif Motif file\n"
" -R, --read-group Limit to just a single read group\n"
" -f, --include-aln-flag Flags to include (like samtools -f)\n"
Expand Down Expand Up @@ -178,7 +178,7 @@ int main(int argc, char** argv) {

#ifndef __APPLE__
// start the timer
//clock_gettime(CLOCK_MONOTONIC, &start);
// clock_gettime(CLOCK_MONOTONIC, &start);
#endif

// parse the command line
Expand Down Expand Up @@ -217,7 +217,7 @@ int main(int argc, char** argv) {
} else if (opt::proc_regions.find(":") != std::string::npos) {
grv_proc_regions.add(SeqLib::GenomicRegion(opt::proc_regions, reader.Header()));
}
grv_proc_regions.createTreeMap();
grv_proc_regions.CreateTreeMap();
}

// open for writing
Expand Down Expand Up @@ -269,10 +269,10 @@ int main(int argc, char** argv) {
std::cerr << "Rules script: " << str << std::endl;
}

SeqLib::ReadFilterCollection rfc;
SeqLib::Filter::ReadFilterCollection rfc;

if (!opt::rules.empty())
rfc = SeqLib::ReadFilterCollection(opt::rules, reader.Header());
rfc = SeqLib::Filter::ReadFilterCollection(opt::rules, reader.Header());

// make sure command_line_reigons makes sense
if (command_line_regions.size() == 2 && command_line_regions[1].all()) {
Expand All @@ -289,7 +289,7 @@ int main(int argc, char** argv) {

// add specific mini rules from command-line
for (auto& i : command_line_regions) {
SeqLib::ReadFilter rf = BuildReadFilterFromCommandLineRegion(i, reader.Header());
SeqLib::Filter::ReadFilter rf = BuildReadFilterFromCommandLineRegion(i, reader.Header());
//SeqLib::MiniRules mr(i, walk.header());
//SeqLib::ReadFilter rf(i, reader.Header());
//mr.pad = i.pad;
Expand Down Expand Up @@ -318,7 +318,7 @@ int main(int argc, char** argv) {

SeqLib::GRC rules_rg = grv_proc_regions; //reader.GetMiniRulesCollection().getAllRegions();

rules_rg.createTreeMap();
rules_rg.CreateTreeMap();

if (grv_proc_regions.size() && rules_rg.size()) { // intersect rules regions with mask regions.
// dont incorporate rules regions if there are any mate-linked regions
Expand Down

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