/*
 * The MIT License
 *
 * Copyright (c) 2009 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package htsjdk.samtools;

import htsjdk.samtools.util.PeekableIterator;

import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Queue;

/**
 * Utility methods for pairs of SAMRecords
 */
public class SamPairUtil {

    /**
     * The possible orientations of paired reads.
     *
     * F = mapped to forward strand
     * R = mapped to reverse strand
     *
     * FR means the read that's mapped to the forward strand comes before the
     * read mapped to the reverse strand when their 5'-end coordinates are
     * compared.
     */
    public static enum PairOrientation
    {
        FR,     // ( 5' --F-->       <--R-- 5'  )  - aka. innie
        RF,     // (   <--R-- 5'   5' --F-->    )  - aka. outie
        TANDEM // ( 5' --F-->   5' --F-->  or  (  <--R-- 5'   <--R-- 5'  )

    }


    /**
     * Computes the pair orientation of the given SAMRecord.
     * @param r
     * @return PairOrientation of the given SAMRecord.
     * @throws IllegalArgumentException If the record is not a paired read, or
     * one or both reads are unmapped.
     */
    public static PairOrientation getPairOrientation(final SAMRecord r)
    {
        final boolean readIsOnReverseStrand = r.getReadNegativeStrandFlag();

        if(r.getReadUnmappedFlag() || !r.getReadPairedFlag() || r.getMateUnmappedFlag()) {
            throw new IllegalArgumentException("Invalid SAMRecord: " + r.getReadName() + ". This method only works for SAMRecords " +
                    "that are paired reads with both reads aligned.");
        }

        if(readIsOnReverseStrand == r.getMateNegativeStrandFlag() )  {
            return PairOrientation.TANDEM;
        }

        final long positiveStrandFivePrimePos = ( readIsOnReverseStrand
                ?  r.getMateAlignmentStart()  //mate's 5' position  ( x---> )
                :  r.getAlignmentStart() );   //read's 5' position  ( x---> )

        final long negativeStrandFivePrimePos = ( readIsOnReverseStrand
                ?  r.getAlignmentEnd()                                   //read's 5' position  ( <---x )
                :  r.getAlignmentStart() + r.getInferredInsertSize() );  //mate's 5' position  ( <---x )

        return ( positiveStrandFivePrimePos < negativeStrandFivePrimePos
                ? PairOrientation.FR
                : PairOrientation.RF );
    }



    // TODO: KT and TF say this is more complicated than what I have here
    public static boolean isProperPair(final SAMRecord firstEnd, final SAMRecord secondEnd,
                                       final List<PairOrientation> expectedOrientations) {
        // are both records mapped?
        if (firstEnd.getReadUnmappedFlag() || secondEnd.getReadUnmappedFlag()) {
            return false;
        }
        if (firstEnd.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
            return false;
        }
        // AND are they both mapped to the same chromosome

        if (!firstEnd.getReferenceName().equals(secondEnd.getReferenceName())) {
            return false;
        }

        // AND is the pair orientation in the set of expected orientations
        final PairOrientation actual = getPairOrientation(firstEnd);
        return expectedOrientations.contains(actual);
    }

    public static void assertMate(final SAMRecord firstOfPair, final SAMRecord secondOfPair) {
        // Validate paired reads arrive as first of pair, then second of pair

        if (firstOfPair == null) {
            throw new SAMException(
                    "First record does not exist - cannot perform mate assertion!");
        } else if (secondOfPair == null) {
            throw new SAMException(
                    firstOfPair.toString() + " is missing its mate");
        } else if (!firstOfPair.getReadPairedFlag()) {
            throw new SAMException(
                    "First record is not marked as paired: " + firstOfPair.toString());
        } else if (!secondOfPair.getReadPairedFlag()) {
            throw new SAMException(
                    "Second record is not marked as paired: " + secondOfPair.toString());
        } else if (!firstOfPair.getFirstOfPairFlag()) {
            throw new SAMException(
                    "First record is not marked as first of pair: " + firstOfPair.toString());
        } else if (!secondOfPair.getSecondOfPairFlag()) {
            throw new SAMException(
                    "Second record is not marked as second of pair: " + secondOfPair.toString());
        } else if (!firstOfPair.getReadName().equals(secondOfPair.getReadName())) {
            throw new SAMException(
                    "First [" + firstOfPair.getReadName() + "] and Second [" +
                            secondOfPair.getReadName() + "] readnames do not match!");
        }
    }

    /**
     * Obtain the secondOfPair mate belonging to the firstOfPair SAMRecord
     * (assumed to be in the next element of the specified samRecordIterator)
     * @param samRecordIterator the iterator assumed to contain the secondOfPair SAMRecord in the
     * next element in the iteration
     * @param firstOfPair the firstOfPair SAMRecord
     * @return the secondOfPair SAMRecord
     * @throws SAMException when the secondOfPair mate cannot be obtained due to assertion failures
     */
    public static SAMRecord obtainAssertedMate(final Iterator<SAMRecord> samRecordIterator,
                                               final SAMRecord firstOfPair) {
        if (samRecordIterator.hasNext()) {
            final SAMRecord secondOfPair = samRecordIterator.next();
            assertMate(firstOfPair, secondOfPair);
            return secondOfPair;
        } else {
            throw new SAMException(
                    "Second record does not exist: " + firstOfPair.getReadName());
        }
    }

    /**
     * Compute SAMRecord insert size
     * @param firstEnd
     * @param secondEnd
     * @return note that when storing insert size on the secondEnd, the return value must be negated.
     */
    public static int computeInsertSize(final SAMRecord firstEnd, final SAMRecord secondEnd) {
        if (firstEnd.getReadUnmappedFlag() || secondEnd.getReadUnmappedFlag()) {
            return 0;
        }
        if (!firstEnd.getReferenceName().equals(secondEnd.getReferenceName())) {
            return 0;
        }

        final int firstEnd5PrimePosition = firstEnd.getReadNegativeStrandFlag()? firstEnd.getAlignmentEnd(): firstEnd.getAlignmentStart();
        final int secondEnd5PrimePosition = secondEnd.getReadNegativeStrandFlag()? secondEnd.getAlignmentEnd(): secondEnd.getAlignmentStart();

        final int adjustment = (secondEnd5PrimePosition >= firstEnd5PrimePosition) ? +1 : -1;
        return secondEnd5PrimePosition - firstEnd5PrimePosition + adjustment;
    }

    /**
     * Write the mate info for two SAMRecords.  This will always clear/remove any mate cigar tag that is present.
     * @param rec1 the first SAM record
     * @param rec2 the second SAM record
     */
    public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2) {
        setMateInfo(rec1, rec2, false);
    }

    /**
     * Write the mate info for two SAMRecords
     * @param rec1 the first SAM record. Must have a non-null SAMFileHeader.
     * @param rec2 the second SAM record. Must have a non-null SAMFileHeader.
     * @param setMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
     */
    public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final boolean setMateCigar) {
        // If neither read is unmapped just set their mate info
        if (!rec1.getReadUnmappedFlag() && !rec2.getReadUnmappedFlag()) {
            rec1.setMateReferenceIndex(rec2.getReferenceIndex());
            rec1.setMateAlignmentStart(rec2.getAlignmentStart());
            rec1.setMateNegativeStrandFlag(rec2.getReadNegativeStrandFlag());
            rec1.setMateUnmappedFlag(false);
            rec1.setAttribute(SAMTag.MQ, rec2.getMappingQuality());

            rec2.setMateReferenceIndex(rec1.getReferenceIndex());
            rec2.setMateAlignmentStart(rec1.getAlignmentStart());
            rec2.setMateNegativeStrandFlag(rec1.getReadNegativeStrandFlag());
            rec2.setMateUnmappedFlag(false);
            rec2.setAttribute(SAMTag.MQ, rec1.getMappingQuality());

            if (setMateCigar) {
                rec1.setAttribute(SAMTag.MC, rec2.getCigarString());
                rec2.setAttribute(SAMTag.MC, rec1.getCigarString());
            }
            else {
                rec1.setAttribute(SAMTag.MC, null);
                rec2.setAttribute(SAMTag.MC, null);
            }
        }
        // Else if they're both unmapped set that straight
        else if (rec1.getReadUnmappedFlag() && rec2.getReadUnmappedFlag()) {
            rec1.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
            rec1.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
            rec1.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
            rec1.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
            rec1.setMateNegativeStrandFlag(rec2.getReadNegativeStrandFlag());
            rec1.setMateUnmappedFlag(true);
            rec1.setAttribute(SAMTag.MQ, null);
            rec1.setAttribute(SAMTag.MC, null);
            rec1.setInferredInsertSize(0);

            rec2.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
            rec2.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
            rec2.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
            rec2.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
            rec2.setMateNegativeStrandFlag(rec1.getReadNegativeStrandFlag());
            rec2.setMateUnmappedFlag(true);
            rec2.setAttribute(SAMTag.MQ, null);
            rec2.setAttribute(SAMTag.MC, null);
            rec2.setInferredInsertSize(0);
        }
        // And if only one is mapped copy it's coordinate information to the mate
        else {
            final SAMRecord mapped   = rec1.getReadUnmappedFlag() ? rec2 : rec1;
            final SAMRecord unmapped = rec1.getReadUnmappedFlag() ? rec1 : rec2;
            unmapped.setReferenceIndex(mapped.getReferenceIndex());
            unmapped.setAlignmentStart(mapped.getAlignmentStart());

            mapped.setMateReferenceIndex(unmapped.getReferenceIndex());
            mapped.setMateAlignmentStart(unmapped.getAlignmentStart());
            mapped.setMateNegativeStrandFlag(unmapped.getReadNegativeStrandFlag());
            mapped.setMateUnmappedFlag(true);
            mapped.setAttribute(SAMTag.MQ, null);
            mapped.setAttribute(SAMTag.MC, null);
            mapped.setInferredInsertSize(0);

            unmapped.setMateReferenceIndex(mapped.getReferenceIndex());
            unmapped.setMateAlignmentStart(mapped.getAlignmentStart());
            unmapped.setMateNegativeStrandFlag(mapped.getReadNegativeStrandFlag());
            unmapped.setMateUnmappedFlag(false);
            unmapped.setAttribute(SAMTag.MQ, mapped.getMappingQuality());
            // For the unmapped read, set mateCigar to the mate's Cigar, since the mate must be mapped
            if (setMateCigar) unmapped.setAttribute(SAMTag.MC, mapped.getCigarString());
            else unmapped.setAttribute(SAMTag.MC, null);
            unmapped.setInferredInsertSize(0);
        }

        final int insertSize = SamPairUtil.computeInsertSize(rec1, rec2);
        rec1.setInferredInsertSize(insertSize);
        rec2.setInferredInsertSize(-insertSize);
    }

    /**
     * Write the mate info for two SAMRecords
     * @param rec1 the first SAM record
     * @param rec2 the second SAM record
     * @param header the SAM file header
     * @param setMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
     * @deprecated use {@link #setMateInfo(SAMRecord, SAMRecord, boolean)} instead
     */
    @Deprecated
    public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final SAMFileHeader header, final boolean setMateCigar) {
        setMateInfo(rec1, rec2, setMateCigar);
    }

    /**
     * Write the mate info for two SAMRecords.  This will always clear/remove any mate cigar tag that is present.
     * @param rec1 the first SAM record
     * @param rec2 the second SAM record
     * @param header the SAM file header
     * @deprecated use {@link #setMateInfo(SAMRecord, SAMRecord)} instead
     */
    @Deprecated
    public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final SAMFileHeader header) {
        setMateInfo(rec1, rec2);
    }

    /**
     * Sets mate pair information appropriately on a supplemental SAMRecord (e.g. from a split alignment)
     * using the primary alignment of the read's mate.
     * @param supplemental a supplemental alignment for the mate pair of the primary supplied
     * @param matePrimary the primary alignment of the the mate pair of the supplemental
     * @param setMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
     */
    public static void setMateInformationOnSupplementalAlignment( final SAMRecord supplemental,
                                                                  final SAMRecord matePrimary,
                                                                  final boolean setMateCigar) {
        supplemental.setMateReferenceIndex(matePrimary.getReferenceIndex());
        supplemental.setMateAlignmentStart(matePrimary.getAlignmentStart());
        supplemental.setMateNegativeStrandFlag(matePrimary.getReadNegativeStrandFlag());
        supplemental.setMateUnmappedFlag(matePrimary.getReadUnmappedFlag());
        supplemental.setInferredInsertSize(-matePrimary.getInferredInsertSize());
        if (setMateCigar && !matePrimary.getReadUnmappedFlag()) {
            supplemental.setAttribute(SAMTag.MC, matePrimary.getCigarString());
        }
        else {
            supplemental.setAttribute(SAMTag.MC, null);
        }
    }

    /**
     * Sets mate pair information appropriately on a supplemental SAMRecord (e.g. from a split alignment)
     * using the primary alignment of the read's mate.
     * @param supplemental a supplemental alignment for the mate pair of the primary supplied
     * @param matePrimary the primary alignment of the the mate pair of the supplemental
     */
    public static void setMateInformationOnSupplementalAlignment( final SAMRecord supplemental,
                                                                  final SAMRecord matePrimary) {
        setMateInformationOnSupplementalAlignment(supplemental, matePrimary, false);
    }

    /**
     * This method will clear any mate cigar already present.
     * @deprecated use {@link #setProperPairAndMateInfo(SAMRecord, SAMRecord, List)} instead
     */
    @Deprecated
    public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
                                                final SAMFileHeader header,
                                                final List<PairOrientation> expectedOrientations) {
        setProperPairAndMateInfo(rec1, rec2, expectedOrientations);
    }

    /**
     * @param addMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
     * @deprecated use {@link #setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)}
     */
    @Deprecated
    public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
                                                final SAMFileHeader header,
                                                final List<PairOrientation> expectedOrientations,
                                                final boolean addMateCigar) {
        setProperPairAndMateInfo(rec1, rec2, expectedOrientations, addMateCigar);
    }

    /**
     * This method will clear any mate cigar already present.
     */
    public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
                                                final List<PairOrientation> expectedOrientations) {
        setProperPairAndMateInfo(rec1, rec2, expectedOrientations, false);
    }

    /**
     * @param addMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
     */
    public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
                                                final List<PairOrientation> expectedOrientations,
                                                final boolean addMateCigar) {
        setMateInfo(rec1, rec2, addMateCigar);
        setProperPairFlags(rec1, rec2, expectedOrientations);
    }

    public static void setProperPairFlags(final SAMRecord rec1, final SAMRecord rec2, final List<PairOrientation> expectedOrientations) {
        final boolean properPair =  (!rec1.getReadUnmappedFlag() && !rec2.getReadUnmappedFlag())
                ? isProperPair(rec1, rec2, expectedOrientations)
                : false;
        rec1.setProperPairFlag(properPair);
        rec2.setProperPairFlag(properPair);
    }

    /**
     * A class to iterate through SAMRecords and set mate information on the given records, and optionally
     * set the mate cigar tag (true by default).
     */
    public static class SetMateInfoIterator extends PeekableIterator<SAMRecord> {

        private final Queue<SAMRecord> records = new LinkedList<SAMRecord>();
        private final boolean setMateCigar;
        private final boolean ignoreMissingMates;
        private long numMateCigarsAdded = 0;

        /**
         * By default, the mate cigar tag is set
         * @param iterator the iterator to wrap
         */
        public SetMateInfoIterator(final Iterator<SAMRecord> iterator) {
            this(iterator, true);
        }

        /**
         * @param iterator the iterator to wrap
         * @param setMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
         */
        public SetMateInfoIterator(final Iterator<SAMRecord> iterator, final boolean setMateCigar) {
            this(iterator, setMateCigar, false);
        }

        /**
         * @param iterator the iterator to wrap
         * @param setMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
         * @param ignoreMissingMates set this to true if we are to ignore missing mates, otherwise an exception will be thrown when a missing mate is encountered
         */
        public SetMateInfoIterator(final Iterator<SAMRecord> iterator, final boolean setMateCigar, final boolean ignoreMissingMates) {
            super(iterator);
            this.setMateCigar = setMateCigar;
            this.ignoreMissingMates = ignoreMissingMates;
        }

        /**
         * @return the current number of mate cigars added.  This could be more than the number of records returned.
         */
        public long getNumMateCigarsAdded() { return this.numMateCigarsAdded; }

        @Override
        public boolean hasNext() {
            return (!records.isEmpty() || super.hasNext());
        }

        /**
         * Populate this.records if necessary.
         */
        private void advance() {

            // No need to advance if we have records remaining
            if (!records.isEmpty()) return;

            /*
              Get all records with the same name, and then identify the canonical first and second end to which we
              want to set mate info.
             */
            SAMRecord firstPrimaryRecord = null, secondPrimaryRecord = null;
            final SAMRecord first = super.peek(); // peek so we consider it in the following loop
            boolean containsSupplementalRecord = false;
            while (super.hasNext() && super.peek().getReadName().equals(first.getReadName())) {
                final SAMRecord record = super.next();
                // We must make sure that we find only one "primary" alignments for each end
                if (record.getReadPairedFlag()) {
                    if (!record.isSecondaryOrSupplementary()) {
                        if (record.getFirstOfPairFlag()) {
                            if (null != firstPrimaryRecord) {
                                throw new SAMException("Found two records that are paired, not supplementary, and first of the pair: " + record.getReadName());
                            }
                            firstPrimaryRecord = record;
                        } else if (record.getSecondOfPairFlag()) {
                            if (null != secondPrimaryRecord) {
                                throw new SAMException("Found two records that are paired, not supplementary, and second of the pair: " + record.getReadName());
                            }
                            secondPrimaryRecord = record;
                        }
                    }
                    if (record.getSupplementaryAlignmentFlag()) containsSupplementalRecord = true;
                }
                records.add(record);
            }
            // TODO: should we check that we do not have a mix of paired and fragment reads?


            // we must find both records to update the mate info
            if (null != firstPrimaryRecord && null != secondPrimaryRecord) {
                // Update mate info
                SamPairUtil.setMateInfo(firstPrimaryRecord, secondPrimaryRecord, this.setMateCigar);
                if (this.setMateCigar) this.numMateCigarsAdded += 2;

                // Set mate information on supplemental records
                if (containsSupplementalRecord) {
                    for (final SAMRecord record : records) {
                        if (record.getReadPairedFlag() && record.getSupplementaryAlignmentFlag()) {
                            if (record.getFirstOfPairFlag()) {
                                SamPairUtil.setMateInformationOnSupplementalAlignment(record, secondPrimaryRecord, this.setMateCigar);
                            } else {
                                SamPairUtil.setMateInformationOnSupplementalAlignment(record, firstPrimaryRecord, this.setMateCigar);
                            }
                            this.numMateCigarsAdded++;
                        }
                    }
                }
            } else if (!this.ignoreMissingMates) {
                if (null != firstPrimaryRecord && firstPrimaryRecord.getReadPairedFlag()) {
                    throw new SAMException("Missing second read of pair: " + firstPrimaryRecord.getReadName());
                } else if (null != secondPrimaryRecord && secondPrimaryRecord.getReadPairedFlag()) {
                    throw new SAMException("Missing first read of pair: " + secondPrimaryRecord.getReadName());
                }
            }
        }

        @Override
        public SAMRecord next() {
            advance();
            if (records.isEmpty()) throw new IllegalStateException("Unexpectedly found an empty record list");
            return this.records.poll();
        }

        @Override
        public SAMRecord peek() {
            advance();
            if (records.isEmpty()) throw new IllegalStateException("Unexpectedly found an empty record list");
            return this.records.peek();
        }
    }
}
