From 14a68596641b12ff74404ec943d90c7e93ba08c8 Mon Sep 17 00:00:00 2001 From: mdcao Date: Thu, 10 May 2018 18:46:29 -0400 Subject: [PATCH] fix bug with generating MD string on https://github.com/isovic/graphmap/issues/90 --- src/alignment/anchored.cc | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/alignment/anchored.cc b/src/alignment/anchored.cc index df13788..4666ae3 100644 --- a/src/alignment/anchored.cc +++ b/src/alignment/anchored.cc @@ -876,7 +876,9 @@ int AnchoredAlignmentNew(AlignmentFunctionType AlignmentFunctionNW, AlignmentFun curr_aln->cigar = AlignmentToCigar((unsigned char *) &(curr_aln->alignment[0]), curr_aln->alignment.size(), parameters->use_extended_cigar); LOG_DEBUG_SPEC("Converting alignment to MD string.\n"); - curr_aln->md = AlignmentToMD((std::vector &) curr_aln->alignment, &index->get_data()[0], final_aln_pos_start); + //curr_aln->md = AlignmentToMD((std::vector &) curr_aln->alignment, &index->get_data()[0], final_aln_pos_start); + //MDC: fixed bug with generating MD + curr_aln->md = AlignmentToMD((std::vector &) curr_aln->alignment, &index->get_data()[0] + index->get_reference_starting_pos()[ref_id], final_aln_pos_start); // printf ("final_aln_pos_start = %ld\n", final_aln_pos_start); // printf ("Query:\n%s\nTarget:\n%s\n", GetSubstring((char *) read->get_data(), read->get_data_length()).c_str(), GetSubstring((char *) index->get_data() + final_aln_pos_start, read->get_data_length()).c_str());