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Merge pull request #74 from andersen-lab/insert_size
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resolves #73
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@gkarthik
gkarthik authored Oct 14, 2020
2 parents f7b6dde + 66e3189 commit 29cf79d
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Showing 7 changed files with 384 additions and 14 deletions.
2 changes: 1 addition & 1 deletion configure.ac
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Expand Up @@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])
AC_INIT([ivar], [1.2.3], [[email protected]])
AC_INIT([ivar], [1.2.4], [[email protected]])
AM_INIT_AUTOMAKE([foreign subdir-objects])
AC_CONFIG_HEADERS([config.h])

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218 changes: 218 additions & 0 deletions data/test_isize.bed
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NC_045512.2 30 54 nCoV-2019_1_LEFT 60 +
NC_045512.2 385 410 nCoV-2019_1_RIGHT 60 -
NC_045512.2 320 342 nCoV-2019_2_LEFT 60 +
NC_045512.2 704 726 nCoV-2019_2_RIGHT 60 -
NC_045512.2 642 664 nCoV-2019_3_LEFT 60 +
NC_045512.2 1004 1028 nCoV-2019_3_RIGHT 60 -
NC_045512.2 943 965 nCoV-2019_4_LEFT 60 +
NC_045512.2 1312 1337 nCoV-2019_4_RIGHT 60 -
NC_045512.2 1242 1264 nCoV-2019_5_LEFT 60 +
NC_045512.2 1623 1651 nCoV-2019_5_RIGHT 60 -
NC_045512.2 1573 1595 nCoV-2019_6_LEFT 60 +
NC_045512.2 1942 1964 nCoV-2019_6_RIGHT 60 -
NC_045512.2 1875 1897 nCoV-2019_7_LEFT 60 +
NC_045512.2 1868 1890 nCoV-2019_7_LEFT_alt0 60 +
NC_045512.2 2247 2269 nCoV-2019_7_RIGHT 60 -
NC_045512.2 2242 2264 nCoV-2019_7_RIGHT_alt5 60 -
NC_045512.2 2181 2205 nCoV-2019_8_LEFT 60 +
NC_045512.2 2568 2592 nCoV-2019_8_RIGHT 60 -
NC_045512.2 2505 2529 nCoV-2019_9_LEFT 60 +
NC_045512.2 2504 2528 nCoV-2019_9_LEFT_alt4 60 +
NC_045512.2 2882 2904 nCoV-2019_9_RIGHT 60 -
NC_045512.2 2880 2902 nCoV-2019_9_RIGHT_alt2 60 -
NC_045512.2 2826 2850 nCoV-2019_10_LEFT 60 +
NC_045512.2 3183 3210 nCoV-2019_10_RIGHT 60 -
NC_045512.2 3144 3166 nCoV-2019_11_LEFT 60 +
NC_045512.2 3507 3531 nCoV-2019_11_RIGHT 60 -
NC_045512.2 3460 3482 nCoV-2019_12_LEFT 60 +
NC_045512.2 3826 3853 nCoV-2019_12_RIGHT 60 -
NC_045512.2 3771 3795 nCoV-2019_13_LEFT 60 +
NC_045512.2 4142 4164 nCoV-2019_13_RIGHT 60 -
NC_045512.2 4054 4077 nCoV-2019_14_LEFT 60 +
NC_045512.2 4044 4068 nCoV-2019_14_LEFT_alt4 60 +
NC_045512.2 4428 4450 nCoV-2019_14_RIGHT 60 -
NC_045512.2 4402 4424 nCoV-2019_14_RIGHT_alt2 60 -
NC_045512.2 4294 4321 nCoV-2019_15_LEFT 60 +
NC_045512.2 4296 4322 nCoV-2019_15_LEFT_alt1 60 +
NC_045512.2 4674 4696 nCoV-2019_15_RIGHT 60 -
NC_045512.2 4666 4689 nCoV-2019_15_RIGHT_alt3 60 -
NC_045512.2 4636 4658 nCoV-2019_16_LEFT 60 +
NC_045512.2 4995 5017 nCoV-2019_16_RIGHT 60 -
NC_045512.2 4939 4966 nCoV-2019_17_LEFT 60 +
NC_045512.2 5296 5321 nCoV-2019_17_RIGHT 60 -
NC_045512.2 5230 5259 nCoV-2019_18_LEFT 60 +
NC_045512.2 5257 5287 nCoV-2019_18_LEFT_alt2 60 +
NC_045512.2 5620 5644 nCoV-2019_18_RIGHT 60 -
NC_045512.2 5620 5643 nCoV-2019_18_RIGHT_alt1 60 -
NC_045512.2 5563 5586 nCoV-2019_19_LEFT 60 +
NC_045512.2 5932 5957 nCoV-2019_19_RIGHT 60 -
NC_045512.2 5867 5894 nCoV-2019_20_LEFT 60 +
NC_045512.2 6247 6272 nCoV-2019_20_RIGHT 60 -
NC_045512.2 6167 6196 nCoV-2019_21_LEFT 60 +
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NC_045512.2 6526 6548 nCoV-2019_21_RIGHT_alt0 60 -
NC_045512.2 6466 6495 nCoV-2019_22_LEFT 60 +
NC_045512.2 6846 6873 nCoV-2019_22_RIGHT 60 -
NC_045512.2 6718 6745 nCoV-2019_23_LEFT 60 +
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NC_045512.2 7035 7058 nCoV-2019_24_LEFT 60 +
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NC_045512.2 7305 7332 nCoV-2019_25_LEFT 60 +
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NC_045512.2 7943 7968 nCoV-2019_27_LEFT 60 +
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NC_045512.2 8249 8275 nCoV-2019_28_LEFT 60 +
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NC_045512.2 8595 8619 nCoV-2019_29_LEFT 60 +
NC_045512.2 8954 8983 nCoV-2019_29_RIGHT 60 -
NC_045512.2 8888 8913 nCoV-2019_30_LEFT 60 +
NC_045512.2 9245 9271 nCoV-2019_30_RIGHT 60 -
NC_045512.2 9204 9226 nCoV-2019_31_LEFT 60 +
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NC_045512.2 9477 9502 nCoV-2019_32_LEFT 60 +
NC_045512.2 9834 9858 nCoV-2019_32_RIGHT 60 -
NC_045512.2 9784 9806 nCoV-2019_33_LEFT 60 +
NC_045512.2 10146 10171 nCoV-2019_33_RIGHT 60 -
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NC_045512.2 10362 10384 nCoV-2019_35_LEFT 60 +
NC_045512.2 10737 10763 nCoV-2019_35_RIGHT 60 -
NC_045512.2 10666 10688 nCoV-2019_36_LEFT 60 +
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NC_045512.2 11306 11331 nCoV-2019_38_LEFT 60 +
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NC_045512.2 11555 11584 nCoV-2019_39_LEFT 60 +
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NC_045512.2 11863 11889 nCoV-2019_40_LEFT 60 +
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NC_045512.2 12110 12133 nCoV-2019_41_LEFT 60 +
NC_045512.2 12465 12490 nCoV-2019_41_RIGHT 60 -
NC_045512.2 12417 12439 nCoV-2019_42_LEFT 60 +
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NC_045512.2 12710 12732 nCoV-2019_43_LEFT 60 +
NC_045512.2 13074 13096 nCoV-2019_43_RIGHT 60 -
NC_045512.2 13005 13027 nCoV-2019_44_LEFT 60 +
NC_045512.2 13007 13029 nCoV-2019_44_LEFT_alt3 60 +
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NC_045512.2 13363 13385 nCoV-2019_44_RIGHT_alt0 60 -
NC_045512.2 13319 13344 nCoV-2019_45_LEFT 60 +
NC_045512.2 13307 13336 nCoV-2019_45_LEFT_alt2 60 +
NC_045512.2 13669 13699 nCoV-2019_45_RIGHT 60 -
NC_045512.2 13660 13689 nCoV-2019_45_RIGHT_alt7 60 -
NC_045512.2 13599 13621 nCoV-2019_46_LEFT 60 +
NC_045512.2 13602 13625 nCoV-2019_46_LEFT_alt1 60 +
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NC_045512.2 13961 13984 nCoV-2019_46_RIGHT_alt2 60 -
NC_045512.2 13918 13946 nCoV-2019_47_LEFT 60 +
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NC_045512.2 14579 14601 nCoV-2019_48_RIGHT 60 -
NC_045512.2 14545 14570 nCoV-2019_49_LEFT 60 +
NC_045512.2 14898 14926 nCoV-2019_49_RIGHT 60 -
NC_045512.2 14865 14895 nCoV-2019_50_LEFT 60 +
NC_045512.2 15224 15246 nCoV-2019_50_RIGHT 60 -
NC_045512.2 15171 15193 nCoV-2019_51_LEFT 60 +
NC_045512.2 15538 15560 nCoV-2019_51_RIGHT 60 -
NC_045512.2 15481 15503 nCoV-2019_52_LEFT 60 +
NC_045512.2 15861 15886 nCoV-2019_52_RIGHT 60 -
NC_045512.2 15827 15851 nCoV-2019_53_LEFT 60 +
NC_045512.2 16186 16209 nCoV-2019_53_RIGHT 60 -
NC_045512.2 16118 16144 nCoV-2019_54_LEFT 60 +
NC_045512.2 16485 16510 nCoV-2019_54_RIGHT 60 -
NC_045512.2 16416 16444 nCoV-2019_55_LEFT 60 +
NC_045512.2 16804 16833 nCoV-2019_55_RIGHT 60 -
NC_045512.2 16748 16770 nCoV-2019_56_LEFT 60 +
NC_045512.2 17130 17152 nCoV-2019_56_RIGHT 60 -
NC_045512.2 17065 17087 nCoV-2019_57_LEFT 60 +
NC_045512.2 17430 17452 nCoV-2019_57_RIGHT 60 -
NC_045512.2 17381 17406 nCoV-2019_58_LEFT 60 +
NC_045512.2 17738 17761 nCoV-2019_58_RIGHT 60 -
NC_045512.2 17674 17697 nCoV-2019_59_LEFT 60 +
NC_045512.2 18036 18062 nCoV-2019_59_RIGHT 60 -
NC_045512.2 17966 17993 nCoV-2019_60_LEFT 60 +
NC_045512.2 18324 18348 nCoV-2019_60_RIGHT 60 -
NC_045512.2 18253 18275 nCoV-2019_61_LEFT 60 +
NC_045512.2 18650 18672 nCoV-2019_61_RIGHT 60 -
NC_045512.2 18596 18618 nCoV-2019_62_LEFT 60 +
NC_045512.2 18957 18979 nCoV-2019_62_RIGHT 60 -
NC_045512.2 18896 18918 nCoV-2019_63_LEFT 60 +
NC_045512.2 19275 19297 nCoV-2019_63_RIGHT 60 -
NC_045512.2 19204 19232 nCoV-2019_64_LEFT 60 +
NC_045512.2 19591 19616 nCoV-2019_64_RIGHT 60 -
NC_045512.2 19548 19570 nCoV-2019_65_LEFT 60 +
NC_045512.2 19911 19939 nCoV-2019_65_RIGHT 60 -
NC_045512.2 19844 19866 nCoV-2019_66_LEFT 60 +
NC_045512.2 20231 20255 nCoV-2019_66_RIGHT 60 -
NC_045512.2 20172 20200 nCoV-2019_67_LEFT 60 +
NC_045512.2 20542 20572 nCoV-2019_67_RIGHT 60 -
NC_045512.2 20472 20496 nCoV-2019_68_LEFT 60 +
NC_045512.2 20867 20890 nCoV-2019_68_RIGHT 60 -
NC_045512.2 20786 20813 nCoV-2019_69_LEFT 60 +
NC_045512.2 21146 21169 nCoV-2019_69_RIGHT 60 -
NC_045512.2 21075 21104 nCoV-2019_70_LEFT 60 +
NC_045512.2 21427 21455 nCoV-2019_70_RIGHT 60 -
NC_045512.2 21357 21386 nCoV-2019_71_LEFT 60 +
NC_045512.2 21716 21743 nCoV-2019_71_RIGHT 60 -
NC_045512.2 21658 21682 nCoV-2019_72_LEFT 60 +
NC_045512.2 22013 22038 nCoV-2019_72_RIGHT 60 -
NC_045512.2 21961 21990 nCoV-2019_73_LEFT 60 +
NC_045512.2 22324 22346 nCoV-2019_73_RIGHT 60 -
NC_045512.2 22262 22290 nCoV-2019_74_LEFT 60 +
NC_045512.2 22626 22650 nCoV-2019_74_RIGHT 60 -
NC_045512.2 22516 22542 nCoV-2019_75_LEFT 60 +
NC_045512.2 22877 22903 nCoV-2019_75_RIGHT 60 -
NC_045512.2 22797 22819 nCoV-2019_76_LEFT 60 +
NC_045512.2 22798 22821 nCoV-2019_76_LEFT_alt3 60 +
NC_045512.2 23192 23214 nCoV-2019_76_RIGHT 60 -
NC_045512.2 23189 23212 nCoV-2019_76_RIGHT_alt0 60 -
NC_045512.2 23122 23144 nCoV-2019_77_LEFT 60 +
NC_045512.2 23500 23522 nCoV-2019_77_RIGHT 60 -
NC_045512.2 23443 23466 nCoV-2019_78_LEFT 60 +
NC_045512.2 23822 23847 nCoV-2019_78_RIGHT 60 -
NC_045512.2 23789 23812 nCoV-2019_79_LEFT 60 +
NC_045512.2 24145 24169 nCoV-2019_79_RIGHT 60 -
NC_045512.2 24078 24100 nCoV-2019_80_LEFT 60 +
NC_045512.2 24443 24467 nCoV-2019_80_RIGHT 60 -
NC_045512.2 24391 24416 nCoV-2019_81_LEFT 60 +
NC_045512.2 24765 24789 nCoV-2019_81_RIGHT 60 -
NC_045512.2 24696 24721 nCoV-2019_82_LEFT 60 +
NC_045512.2 25052 25076 nCoV-2019_82_RIGHT 60 -
NC_045512.2 24978 25003 nCoV-2019_83_LEFT 60 +
NC_045512.2 25347 25369 nCoV-2019_83_RIGHT 60 -
NC_045512.2 25279 25301 nCoV-2019_84_LEFT 60 +
NC_045512.2 25646 25673 nCoV-2019_84_RIGHT 60 -
NC_045512.2 25601 25623 nCoV-2019_85_LEFT 60 +
NC_045512.2 25969 25994 nCoV-2019_85_RIGHT 60 -
NC_045512.2 25902 25924 nCoV-2019_86_LEFT 60 +
NC_045512.2 26290 26315 nCoV-2019_86_RIGHT 60 -
NC_045512.2 26197 26219 nCoV-2019_87_LEFT 60 +
NC_045512.2 26566 26590 nCoV-2019_87_RIGHT 60 -
NC_045512.2 26520 26542 nCoV-2019_88_LEFT 60 +
NC_045512.2 26890 26913 nCoV-2019_88_RIGHT 60 -
NC_045512.2 26835 26857 nCoV-2019_89_LEFT 60 +
NC_045512.2 26838 26860 nCoV-2019_89_LEFT_alt2 60 +
NC_045512.2 27202 27227 nCoV-2019_89_RIGHT 60 -
NC_045512.2 27190 27215 nCoV-2019_89_RIGHT_alt4 60 -
NC_045512.2 27141 27164 nCoV-2019_90_LEFT 60 +
NC_045512.2 27511 27533 nCoV-2019_90_RIGHT 60 -
NC_045512.2 27446 27471 nCoV-2019_91_LEFT 60 +
NC_045512.2 27825 27854 nCoV-2019_91_RIGHT 60 -
NC_045512.2 27784 27808 nCoV-2019_92_LEFT 60 +
NC_045512.2 28145 28172 nCoV-2019_92_RIGHT 60 -
NC_045512.2 28081 28104 nCoV-2019_93_LEFT 60 +
NC_045512.2 28442 28464 nCoV-2019_93_RIGHT 60 -
NC_045512.2 28394 28416 nCoV-2019_94_LEFT 60 +
NC_045512.2 28756 28779 nCoV-2019_94_RIGHT 60 -
NC_045512.2 28677 28699 nCoV-2019_95_LEFT 60 +
NC_045512.2 29041 29063 nCoV-2019_95_RIGHT 60 -
NC_045512.2 28985 29007 nCoV-2019_96_LEFT 60 +
NC_045512.2 29356 29378 nCoV-2019_96_RIGHT 60 -
NC_045512.2 29288 29316 nCoV-2019_97_LEFT 60 +
NC_045512.2 29665 29693 nCoV-2019_97_RIGHT 60 -
NC_045512.2 29486 29510 nCoV-2019_98_LEFT 60 +
NC_045512.2 29836 29866 nCoV-2019_98_RIGHT 60 -
Binary file added data/test_isize.sorted.bam
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2 changes: 1 addition & 1 deletion src/ivar.cpp
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Expand Up @@ -16,7 +16,7 @@
#include "suffix_tree.h"
#include "get_common_variants.h"

const std::string VERSION = "1.2.3";
const std::string VERSION = "1.2.4";

struct args_t {
std::string bam; // -i
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38 changes: 28 additions & 10 deletions src/trim_primer_quality.cpp
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Expand Up @@ -166,15 +166,15 @@ cigar_ primer_trim(bam1_t *r, int32_t new_pos, bool unpaired_rev = false){
uint32_t i = 0, j = 0;
int max_del_len = 0, cig, temp, del_len = 0;
bool reverse = false;
if((r->core.flag&BAM_FPAIRED) != 0){ // If paired
if (bam_is_rev(r)){
if((r->core.flag&BAM_FPAIRED) != 0 && !(abs(r->core.isize) <= abs(r->core.l_qseq))){ // If paired and isize > read length
if (bam_is_rev(r)){ // If -ve strand (?)
max_del_len = bam_cigar2qlen(r->core.n_cigar, bam_get_cigar(r)) - get_pos_on_query(cigar, r->core.n_cigar, new_pos, r->core.pos) - 1;
reverse_cigar(cigar, r->core.n_cigar);
reverse = true;
} else {
max_del_len = get_pos_on_query(cigar, r->core.n_cigar, new_pos, r->core.pos);
}
} else { // Unpaired
} else { // trim without considering pairing
if(unpaired_rev){
max_del_len = bam_cigar2qlen(r->core.n_cigar, bam_get_cigar(r)) - get_pos_on_query(cigar, r->core.n_cigar, new_pos, r->core.pos) - 1;
reverse_cigar(cigar, r->core.n_cigar);
Expand Down Expand Up @@ -206,7 +206,7 @@ cigar_ primer_trim(bam1_t *r, int32_t new_pos, bool unpaired_rev = false){
ncigar[j] = bam_cigar_gen(n, BAM_CSOFT_CLIP);
} else if (del_len < n && del_len > 0){
ncigar[j] = bam_cigar_gen(del_len, BAM_CSOFT_CLIP);
} else if (del_len == 0) { // Ading insertions before start position of read
} else if (del_len == 0) { // Adding insertions before start position of read
ncigar[j] = bam_cigar_gen(n, BAM_CSOFT_CLIP);
j++;
i++;
Expand Down Expand Up @@ -409,24 +409,32 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,
init_cigar(&t);
uint32_t primer_trim_count = 0, no_primer_counter = 0, low_quality = 0;
bool unmapped_flag = false;
uint32_t failed_frag_size = 0;
uint32_t unmapped_counter = 0;
primer cand_primer;
std::vector<primer> overlapping_primers;
std::vector<primer>::iterator cit;
bool primer_trimmed = false;
//Iterate through reads
while(sam_itr_next(in, iter, aln) >= 0) {
unmapped_flag = false;
primer_trimmed = false;
if((aln->core.flag&BAM_FUNMAP) == 0){
if((aln->core.flag&BAM_FPAIRED) != 0){ // If paired
if((aln->core.flag&BAM_FUNMAP) == 0){ // If mapped
if((aln->core.flag&BAM_FPAIRED) != 0 && !(abs(aln->core.isize) <= abs(aln->core.l_qseq))){ // If paired
/*
if((abs(aln->core.isize) <= abs(aln->core.l_qseq))){
failed_frag_size++;
continue;
}
*/
get_overlapping_primers(aln, primers, overlapping_primers);
if(overlapping_primers.size() > 0){
if(overlapping_primers.size() > 0){ // If read starts before overlapping regions (?)
primer_trimmed = true;
if(bam_is_rev(aln)){ // Reverse
cand_primer = get_min_start(overlapping_primers);
cand_primer = get_min_start(overlapping_primers); // fetch reverse primer (?)
t = primer_trim(aln, cand_primer.get_start() - 1, false);
} else { // Forward
cand_primer = get_max_end(overlapping_primers);
cand_primer = get_max_end(overlapping_primers); // fetch forward primer (?)
t = primer_trim(aln, cand_primer.get_end() + 1, false);
aln->core.pos += t.start_pos;
}
Expand All @@ -438,18 +446,22 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,
cit->add_read_count(1);
}
t = quality_trim(aln, min_qual, sliding_window); // Quality Trimming
if(bam_is_rev(aln))
if(bam_is_rev(aln)) // if reverse strand
aln->core.pos = t.start_pos;
condense_cigar(&t);
// aln->core.pos += t.start_pos;
replace_cigar(aln, t.nlength, t.cigar);
} else { // Unpaired reads: Might be stitched reads
if(abs(aln->core.isize) <= abs(aln->core.l_qseq)){
failed_frag_size++;
}
// Forward primer
get_overlapping_primers(aln, primers, overlapping_primers, false);
if(overlapping_primers.size() > 0){
primer_trimmed = true;
cand_primer = get_max_end(overlapping_primers);
t = primer_trim(aln, cand_primer.get_end() + 1, false);
// Update read's left-most coordinate (?)
aln->core.pos += t.start_pos;
replace_cigar(aln, t.nlength, t.cigar);
// Add count to primer
Expand Down Expand Up @@ -545,6 +557,12 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,
if(unmapped_counter > 0){
std::cout << unmapped_counter << " unmapped reads were not written to file." << std::endl;
}
if(failed_frag_size > 0){
std::cout << round_int(failed_frag_size, mapped)
<< "% (" << failed_frag_size
<< ") of reads had their insert size smaller than their read length"
<< std::endl;
}

error:
if (retval) std::cout << "Not able to write to BAM" << std::endl;
Expand Down
5 changes: 3 additions & 2 deletions tests/Makefile.am
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ LIBS = -lhts -lz -lpthread

CXXFLAGS = -g -std=c++11 -Wall -Wextra -Werror

TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases
check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases
TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim
check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim
check_primer_trim_SOURCES = test_primer_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp
check_trim_SOURCES = test_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp
check_quality_trim_SOURCES = check_quality_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp
Expand All @@ -19,3 +19,4 @@ check_getmasked_SOURCES = test_getmasked.cpp ../src/get_masked_amplicons.cpp ../
check_removereads_SOURCES = test_removereads.cpp ../src/remove_reads_from_amplicon.cpp ../src/primer_bed.cpp ../src/trim_primer_quality.cpp
check_unpaired_trim_SOURCES = test_unpaired_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp
check_primer_trim_edge_cases_SOURCES = test_primer_trim_edge_cases.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp
check_isize_trim_SOURCES = test_isize_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp
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