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Enable prefix-grouping for one-to-one filtering #66

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merged 2 commits into from
Jan 2, 2024
Merged

Enable prefix-grouping for one-to-one filtering #66

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cde5a6f
Enable skipPrefix for one-to-one mode
bkille Dec 23, 2023
e83483f
update version
bkille Dec 24, 2023
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98 changes: 72 additions & 26 deletions src/map/include/computeMap.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
#include <limits>
#include <vector>
#include <algorithm>
#include <iterator>
#include <unordered_map>
#include <fstream>
#include <zlib.h>
Expand Down Expand Up @@ -356,17 +357,49 @@ namespace skch
//Filter over reference axis and report the mappings
if (param.filterMode == filter::ONETOONE)
{
skch::Filter::ref::filterMappings(allReadMappings, this->refSketch,
param.numMappingsForSegment - 1
// (input->len < param.segLength ? param.shortSecondaryToKeep : param.secondaryToKeep)
);
// how many secondary mappings to keep
int n_mappings = param.numMappingsForSegment - 1;

// Group sequences by query prefix, then pass to ref filter
auto subrange_begin = allReadMappings.begin();
auto subrange_end = allReadMappings.begin();
MappingResultsVector_t tmpMappings;
MappingResultsVector_t filteredMappings;

while (subrange_end != allReadMappings.end())
{
if (param.skip_prefix)
{
int currGroup = this->getRefGroup(qmetadata[subrange_begin->querySeqId].name);
subrange_end = std::find_if_not(subrange_begin, allReadMappings.end(), [this, currGroup] (const auto& allReadMappings_candidate) {
return currGroup == this->getRefGroup(this->qmetadata[allReadMappings_candidate.querySeqId].name);
});
}
else
{
subrange_end = allReadMappings.end();
}
tmpMappings.insert(
tmpMappings.end(),
std::make_move_iterator(subrange_begin),
std::make_move_iterator(subrange_end));

// tmpMappings now contains mappings from one group of query sequences to all reference groups
// we now run filterByGroup, which filters based on the reference group.
filterByGroup(tmpMappings, filteredMappings, n_mappings, true);
tmpMappings.clear();
subrange_begin = subrange_end;
}
allReadMappings = std::move(filteredMappings);

//Re-sort mappings by input order of query sequences
//This order may be needed for any post analysis of output
std::sort(allReadMappings.begin(), allReadMappings.end(), [](const MappingResult &a, const MappingResult &b)
{
return (a.querySeqId < b.querySeqId);
});
std::sort(
allReadMappings.begin(), allReadMappings.end(),
[](const MappingResult &a, const MappingResult &b) {
return std::tie(a.querySeqId, a.queryStartPos, a.refSeqId, a.refStartPos)
< std::tie(b.querySeqId, b.queryStartPos, b.refSeqId, b.refStartPos);
});

reportReadMappings(allReadMappings, "", outstrm);
}
Expand Down Expand Up @@ -460,17 +493,19 @@ namespace skch
}

/**
* @brief helper to main filtering function
* @details filters mappings by group
* @param[in] input unfiltered mappings
* @param[in] output filtered mappings
* @param[in] input num mappings per segment
* @return void
* @brief helper to main filtering function
* @details filters mappings by group
* @param[in] input unfiltered mappings
* @param[in] output filtered mappings
* @param[in] n_mappings num mappings per segment
* @param[in] filter_ref use Filter::ref instead of Filter::query
* @return void
*/
void filterByGroup(
MappingResultsVector_t &unfilteredMappings,
MappingResultsVector_t &filteredMappings,
int n_mappings)
int n_mappings,
bool filter_ref)
{
filteredMappings.reserve(unfilteredMappings.size());

Expand All @@ -480,6 +515,7 @@ namespace skch
auto subrange_end = unfilteredMappings.begin();
if (param.filterMode == filter::MAP || param.filterMode == filter::ONETOONE)
{
std::vector<skch::MappingResult> tmpMappings;
while (subrange_end != unfilteredMappings.end())
{
if (param.skip_prefix)
Expand All @@ -493,13 +529,25 @@ namespace skch
{
subrange_end = unfilteredMappings.end();
}
// TODO why are we filtering these before merging?
std::vector<skch::MappingResult> tmpMappings(std::distance(subrange_begin, subrange_end));
std::move(subrange_begin, subrange_end, tmpMappings.begin());
tmpMappings.insert(
tmpMappings.end(),
std::make_move_iterator(subrange_begin),
std::make_move_iterator(subrange_end));
std::sort(tmpMappings.begin(), tmpMappings.end(), [](const auto& a, const auto& b)
{ return std::tie(a.queryStartPos, a.refSeqId, a.refStartPos) < std::tie(b.queryStartPos, b.refSeqId, b.refStartPos); });
skch::Filter::query::filterMappings(tmpMappings, n_mappings);
std::move(tmpMappings.begin(), tmpMappings.end(), std::back_inserter(filteredMappings));
if (filter_ref)
{
skch::Filter::ref::filterMappings(tmpMappings, this->refSketch, n_mappings);
}
else
{
skch::Filter::query::filterMappings(tmpMappings, n_mappings);
}
filteredMappings.insert(
filteredMappings.end(),
std::make_move_iterator(tmpMappings.begin()),
std::make_move_iterator(tmpMappings.end()));
tmpMappings.clear();
subrange_begin = subrange_end;
}
}
Expand All @@ -509,8 +557,6 @@ namespace skch
[](const MappingResult &a, const MappingResult &b) {
return std::tie(a.queryStartPos, a.refSeqId, a.refStartPos)
< std::tie(b.queryStartPos, b.refSeqId, b.refStartPos);
//return std::tie(a.refSeqId, a.refStartPos, a.queryStartPos)
//< std::tie(b.refSeqId, b.refStartPos, b.queryStartPos);
});
}

Expand Down Expand Up @@ -644,10 +690,10 @@ namespace skch
}

if (param.filterMode == filter::MAP || param.filterMode == filter::ONETOONE) {
MappingResultsVector_t tempMappings;
tempMappings.reserve(output->readMappings.size());
filterByGroup(unfilteredMappings, tempMappings, n_mappings);
std::swap(tempMappings, unfilteredMappings);
MappingResultsVector_t tmpMappings;
tmpMappings.reserve(output->readMappings.size());
filterByGroup(unfilteredMappings, tmpMappings, n_mappings, false);
unfilteredMappings = std::move(tmpMappings);
}

std::swap(output->readMappings, unfilteredMappings);
Expand Down
2 changes: 1 addition & 1 deletion src/map/include/map_parameters.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ float confidence_interval = 0.95; // Confidence interval to re
float percentage_identity = 0.85; // Percent identity in the mapping step
float ANIDiff = 0.0; // Stage 1 ANI diff threshold
float ANIDiffConf = 0.999; // ANI diff confidence
std::string VERSION = "3.1.2"; // Version of MashMap
std::string VERSION = "3.1.3"; // Version of MashMap
}
}

Expand Down
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