From 2141fa6ea7d3f152880768a1120e4209472f50b9 Mon Sep 17 00:00:00 2001 From: cmaceves Date: Tue, 29 Mar 2022 14:16:33 -0700 Subject: [PATCH 1/5] trim until first base that consumes the reference --- src/trim_primer_quality.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/trim_primer_quality.cpp b/src/trim_primer_quality.cpp index 899c5d67..1747994b 100755 --- a/src/trim_primer_quality.cpp +++ b/src/trim_primer_quality.cpp @@ -221,7 +221,8 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r ncigar[j] = bam_cigar_gen(n, cig); j++; } - if(del_len ==0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_type(ncigar[j-1]) & 2)){ // After soft clipping of query complete, keep incrementing start_pos until first base that consumes both query and ref + if (del_len ==0 && (bam_cigar_type(ncigar[j-1])&1)){ + //if(del_len ==0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_type(ncigar[j-1]) & 2)){ // After soft clipping of query complete, keep incrementing start_pos until first base that consumes both query and ref pos_start = true; } } From b0b8dc5f7f5c7225a83d0b29ebd36fca3f7cafa5 Mon Sep 17 00:00:00 2001 From: cmaceves Date: Mon, 4 Apr 2022 14:01:48 -0700 Subject: [PATCH 2/5] add in more specific condition for soft clips --- src/trim_primer_quality.cpp | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/trim_primer_quality.cpp b/src/trim_primer_quality.cpp index 1747994b..7a13374b 100755 --- a/src/trim_primer_quality.cpp +++ b/src/trim_primer_quality.cpp @@ -221,11 +221,14 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r ncigar[j] = bam_cigar_gen(n, cig); j++; } - if (del_len ==0 && (bam_cigar_type(ncigar[j-1])&1)){ + if(del_len == 0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_op(ncigar[j-1]) != 4)){ //if(del_len ==0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_type(ncigar[j-1]) & 2)){ // After soft clipping of query complete, keep incrementing start_pos until first base that consumes both query and ref - pos_start = true; + pos_start = true; } } + + //deletions consume the reference but not the query, + //insertions consume the query but not the reference if((bam_cigar_type(cig) & 2)) { // Consumes reference but not query start_pos += ref_add; } @@ -234,6 +237,7 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r if(reverse){ reverse_cigar(ncigar, j); } + return { ncigar, true, From a1ab083132820e79490ad1fd72004e46f63c49e4 Mon Sep 17 00:00:00 2001 From: cmaceves Date: Tue, 19 Apr 2022 09:30:20 -0700 Subject: [PATCH 3/5] changing both tests and primer trim to allow leading deletions --- src/trim_primer_quality.cpp | 34 ++++++++++++++++++++++++++++++++-- tests/test_primer_trim.cpp | 23 ++++++++++++----------- 2 files changed, 44 insertions(+), 13 deletions(-) diff --git a/src/trim_primer_quality.cpp b/src/trim_primer_quality.cpp index 7a13374b..6e01f3ee 100755 --- a/src/trim_primer_quality.cpp +++ b/src/trim_primer_quality.cpp @@ -187,6 +187,7 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r int32_t n, start_pos = 0, ref_add = 0; bool pos_start = false; del_len = max_del_len; + std::cout << "primer type " << reverse << "\n"; while(i < r->core.n_cigar){ if (del_len == 0 && pos_start){ // No more bases on query to soft clip ncigar[j] = cigar[i]; @@ -200,7 +201,21 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r pos_start = true; continue; } + + //add the condition that we have a leading deletion + if(cig == 2 && del_len == 0){ + ncigar[j] = cigar[i]; + pos_start = true; + i++; + j++; + //if(reverse==0){ + // start_pos+=bam_cigar_oplen(cigar[i]); + //} + continue; + } + ref_add = n; + std::cout << "n " << n << " " << cig << "\n"; if ((bam_cigar_type(cig) & 1)){ // Consumes Query if(del_len >= n ){ ncigar[j] = bam_cigar_gen(n, BAM_CSOFT_CLIP); @@ -221,8 +236,15 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r ncigar[j] = bam_cigar_gen(n, cig); j++; } - if(del_len == 0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_op(ncigar[j-1]) != 4)){ - //if(del_len ==0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_type(ncigar[j-1]) & 2)){ // After soft clipping of query complete, keep incrementing start_pos until first base that consumes both query and ref + //add the condition that we have a leading deletion + if(cig == 2 && del_len == 0){ + ncigar[j] = cigar[i]; + pos_start = true; + i++; + j++; + } + + if(del_len ==0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_type(ncigar[j-1]) & 2)){ // After soft clipping of query complete, keep incrementing start_pos until first base that consumes both query and ref pos_start = true; } } @@ -230,10 +252,18 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r //deletions consume the reference but not the query, //insertions consume the query but not the reference if((bam_cigar_type(cig) & 2)) { // Consumes reference but not query + std::cout << "here " << ref_add << " " << start_pos << " " << cig << "\n"; start_pos += ref_add; } i++; } + + uint32_t p=0; + while(p < j){ + std::cout << bam_cigar_op(ncigar[p]) << " " << bam_cigar_oplen(ncigar[p]) <<"\n"; + p++; + } + std::cout << "start pos " << start_pos << "\n"; if(reverse){ reverse_cigar(ncigar, j); } diff --git a/tests/test_primer_trim.cpp b/tests/test_primer_trim.cpp index 4bede7cf..21179603 100755 --- a/tests/test_primer_trim.cpp +++ b/tests/test_primer_trim.cpp @@ -37,29 +37,29 @@ int main(){ int primer_indices[] = {0, 0, 7, 7, 6}; uint8_t cigar_flag[5][11] = { {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH}, - {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH}, - {BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP}, + {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH}, + {BAM_CMATCH, BAM_CPAD, BAM_CDEL, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP}, {BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP}, {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH} }; uint32_t cigar_len[5][11] = { {6, 5, 1, 139}, - {24, 3, 1, 1, 4, 114}, - {121, 4, 1, 1, 11, 6}, + {24, 3, 1, 1, 4, 1, 1, 1,114}, //change this + {121, 1, 4, 4, 1, 1, 11, 6}, //change this {103, 1, 10,1,13, 24}, {23, 18, 3, 57, 1, 10, 1, 39} }; uint32_t read_start_pos[5] = { - 30, 31, 231, 249, 274 + 30, 29, 231, 249, 274 //also change }; uint8_t condense_cigar_flag[5][8] = { {BAM_CSOFT_CLIP, BAM_CMATCH}, - {BAM_CSOFT_CLIP, BAM_CMATCH}, - {BAM_CMATCH, BAM_CSOFT_CLIP}, + {BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH}, //change this + {BAM_CMATCH, BAM_CPAD, BAM_CDEL, BAM_CSOFT_CLIP}, //change this {BAM_CMATCH, BAM_CSOFT_CLIP}, {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH} }; - uint32_t condense_cigar_len[5][8] = {{12, 139}, {33, 114}, {121, 23}, {103, 49}, {23, 18,3, 57, 1, 10, 1, 39}}; + uint32_t condense_cigar_len[5][8] = {{12, 139}, {33, 1,1,1,114}, {121, 1, 4, 23}, {103, 49}, {23, 18,3, 57, 1, 10, 1, 39}}; unsigned int overlapping_primer_sizes[] = {0, 2, 2, 0, 0, 0, 0, 2, 2, 1}; int ctr = 0; std::vector overlapping_primers; @@ -100,11 +100,12 @@ int main(){ cigar = bam_get_cigar(aln); for (uint i = 0; i < t.nlength; ++i){ if(((cigar[i]) & BAM_CIGAR_MASK) != cigar_flag[primer_ctr][i]){ + std::cout << bam_cigar_op(cigar[i]) << " " << bam_cigar_oplen(cigar[i]) << " i " << i << "\n"; success = -1; std::cout << "Cigar flag didn't match for " << cand_primer.get_indice() << " ! Expected " << (uint) cigar_flag[primer_ctr][i] << " " << "Got " << ((cigar[i]) & BAM_CIGAR_MASK) << std::endl; } if((((cigar[i]) >> BAM_CIGAR_SHIFT)) != cigar_len[primer_ctr][i]){ - success = -1; + success = -1; std::cout << "Cigar length didn't match for " << bam_get_qname(aln) << " ! Expected " << (uint) cigar_len[primer_ctr][i] << " " << "Got " << ((cigar[i]) >> BAM_CIGAR_SHIFT) << std::endl; } } @@ -117,10 +118,10 @@ int main(){ for (uint i = 0; i < t.nlength; ++i){ if(((cigar[i]) & BAM_CIGAR_MASK) != condense_cigar_flag[primer_ctr][i]){ success = -1; - std::cout << "Cigar flag didn't match! Expected " << condense_cigar_flag[primer_ctr][i] << " " << "Got " << ((cigar[i]) & BAM_CIGAR_MASK) << std::endl; + std::cout << "Cigar flag didn't match! Expected " << condense_cigar_flag[primer_ctr][i] << " " << "Got " << ((cigar[i]) & BAM_CIGAR_MASK) << std::endl; } if((((cigar[i]) >> BAM_CIGAR_SHIFT)) != condense_cigar_len[primer_ctr][i]){ - success = -1; + success = -1; std::cout << "Cigar length didn't match after condense! Expected " << condense_cigar_len[primer_ctr][i] << " " << "Got " << ((cigar[i]) >> BAM_CIGAR_SHIFT) << std::endl; } } From e0df8af7462a879b82ece82cbe12055835b592f6 Mon Sep 17 00:00:00 2001 From: cmaceves Date: Tue, 19 Apr 2022 10:44:26 -0700 Subject: [PATCH 4/5] updating unpaired test and removing excess print lines --- src/trim_primer_quality.cpp | 13 +++++-------- tests/test_unpaired_trim.cpp | 24 ++++++++++++------------ 2 files changed, 17 insertions(+), 20 deletions(-) diff --git a/src/trim_primer_quality.cpp b/src/trim_primer_quality.cpp index 6e01f3ee..73829103 100755 --- a/src/trim_primer_quality.cpp +++ b/src/trim_primer_quality.cpp @@ -187,7 +187,7 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r int32_t n, start_pos = 0, ref_add = 0; bool pos_start = false; del_len = max_del_len; - std::cout << "primer type " << reverse << "\n"; + while(i < r->core.n_cigar){ if (del_len == 0 && pos_start){ // No more bases on query to soft clip ncigar[j] = cigar[i]; @@ -208,14 +208,11 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r pos_start = true; i++; j++; - //if(reverse==0){ - // start_pos+=bam_cigar_oplen(cigar[i]); - //} continue; } ref_add = n; - std::cout << "n " << n << " " << cig << "\n"; + if ((bam_cigar_type(cig) & 1)){ // Consumes Query if(del_len >= n ){ ncigar[j] = bam_cigar_gen(n, BAM_CSOFT_CLIP); @@ -252,7 +249,7 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r //deletions consume the reference but not the query, //insertions consume the query but not the reference if((bam_cigar_type(cig) & 2)) { // Consumes reference but not query - std::cout << "here " << ref_add << " " << start_pos << " " << cig << "\n"; + //std::cout << "ref add " << ref_add << " " << start_pos << " " << cig << "\n"; start_pos += ref_add; } i++; @@ -263,10 +260,10 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r std::cout << bam_cigar_op(ncigar[p]) << " " << bam_cigar_oplen(ncigar[p]) <<"\n"; p++; } - std::cout << "start pos " << start_pos << "\n"; + /*std::cout << "start pos " << start_pos << "\n"; if(reverse){ reverse_cigar(ncigar, j); - } + }*/ return { ncigar, diff --git a/tests/test_unpaired_trim.cpp b/tests/test_unpaired_trim.cpp index c4451167..a07b39df 100755 --- a/tests/test_unpaired_trim.cpp +++ b/tests/test_unpaired_trim.cpp @@ -41,35 +41,35 @@ int main(){ int primer_ctr = 0; int forward_primer_indices[] = {1, 1, 5, 5, 6}; int rev_primer_indices[] = {3, -1, -1, -1, 4}; - uint8_t cigar_flag[5][16] = { - {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP}, // 3S15M5D2M1D14M1I56M1P6M3P93M2D4M2I8M + uint8_t cigar_flag[5][17] = { + {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CDEL, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP}, // 3S15M5D2M1D14M1I56M1P6M3P93M2D4M2I8M {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}, {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP}, - {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}, + {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}, {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP} }; - uint32_t cigar_len[5][16] = { - {3, 15, 2, 1, 14, 1, 56, 1, 6, 3, 93, 2, 1, 3, 2, 8}, + uint32_t cigar_len[5][17] = { + {3, 15, 5, 2, 1, 14, 1, 56, 1, 6, 3, 93, 2, 1, 3, 2, 8}, //change here {1, 19, 1, 56, 1, 6, 3, 99, 2, 65}, {8, 13, 1, 6, 3, 99, 2, 62, 3}, - {9, 10, 3, 97, 2, 26}, + {9, 10, 3, 3, 3, 2, 97, 2, 26}, //change here {18, 71, 2, 89, 18} }; uint32_t read_start_pos[5] = { - 94, 92, 173, 175, 201 + 89, 92, 173, 170, 201 }; uint8_t condense_cigar_flag[5][14] = { - {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP}, + {BAM_CSOFT_CLIP, BAM_CDEL, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP}, {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}, {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP}, - {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}, + {BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}, //change here {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP} }; - uint32_t condense_cigar_len[5][13] = { - {18, 2, 1, 14,1, 56, 1, 6, 3, 93, 2, 1, 13}, + uint32_t condense_cigar_len[5][14] = { + {18, 5, 2, 1, 14,1, 56, 1, 6, 3, 93, 2, 1, 13}, //change here {1, 19, 1, 56, 1, 6, 3, 99, 2, 65}, {31, 99, 2, 62, 3}, - {22, 97, 2, 26}, + {22, 3, 3, 2, 97, 2, 26}, //change here {18, 71, 2, 89, 18} }; unsigned int fwd_overlapping_primer_sizes[] = {2, 1, 1, 1, 1}; From c9522c3406f7f82f4696ec1b3a4df621be72c3a2 Mon Sep 17 00:00:00 2001 From: cmaceves Date: Tue, 19 Apr 2022 10:49:11 -0700 Subject: [PATCH 5/5] fixing incorrectly commented out lines --- src/trim_primer_quality.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/trim_primer_quality.cpp b/src/trim_primer_quality.cpp index 73829103..37d53e6d 100755 --- a/src/trim_primer_quality.cpp +++ b/src/trim_primer_quality.cpp @@ -187,7 +187,7 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r int32_t n, start_pos = 0, ref_add = 0; bool pos_start = false; del_len = max_del_len; - + while(i < r->core.n_cigar){ if (del_len == 0 && pos_start){ // No more bases on query to soft clip ncigar[j] = cigar[i]; @@ -255,15 +255,15 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r i++; } - uint32_t p=0; + /*uint32_t p=0; while(p < j){ std::cout << bam_cigar_op(ncigar[p]) << " " << bam_cigar_oplen(ncigar[p]) <<"\n"; p++; - } - /*std::cout << "start pos " << start_pos << "\n"; + }*/ + //std::cout << "start pos " << start_pos << "\n"; if(reverse){ reverse_cigar(ncigar, j); - }*/ + } return { ncigar,