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Commit 70c6be33 authored by Veronique Legrand's avatar Veronique Legrand
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bugfix : selected reads are now written in decreasing order of quality score

parent 959bfc17
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...@@ -20,7 +20,7 @@ using namespace std; ...@@ -20,7 +20,7 @@ using namespace std;
// TODO this looks a little bit like getDnaStr in read_utils.cpp. Some refactoring could be useful. Think about // TODO this looks a little bit like getDnaStr in read_utils.cpp. Some refactoring could be useful. Think about
// classes to encapsulate that without decreasing perfs. // classes to encapsulate that without decreasing perfs.
void writeFilteredFastq(FqBaseBackend* map_id_backend[],int nb_be, const srp& io_sr){ void writeFilteredFastq(FqBaseBackend* map_id_backend[],int nb_be, const srp& io_sr){
srp::const_iterator it; srp::const_reverse_iterator it;
i_dim::const_iterator it_offs; i_dim::const_iterator it_offs;
k_dim::const_iterator it_struct; k_dim::const_iterator it_struct;
...@@ -35,7 +35,7 @@ void writeFilteredFastq(FqBaseBackend* map_id_backend[],int nb_be, const srp& io ...@@ -35,7 +35,7 @@ void writeFilteredFastq(FqBaseBackend* map_id_backend[],int nb_be, const srp& io
map_id_backend[i]->openOutputFile(); map_id_backend[i]->openOutputFile();
} }
for (it=io_sr.begin(); it!=io_sr.end(); ++it) { for (it=io_sr.rbegin(); it!=io_sr.rend(); ++it) {
for (it_offs=it->second.begin();it_offs!=it->second.end();it_offs++) { for (it_offs=it->second.begin();it_offs!=it->second.end();it_offs++) {
unsigned long j=it_offs->first; unsigned long j=it_offs->first;
for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) { for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
......
...@@ -21,35 +21,37 @@ using namespace std; ...@@ -21,35 +21,37 @@ using namespace std;
#define DEBUG #define DEBUG
char expected_content_PE1 []="@SRR1222430.3 3 length=236\n\
char expected_content_PE1 []="@SRR1222430.1 1 length=251\n\ CAAACACCTGACGCGGTTCCAGCAGGTACTCCTGCACGCCAATTTCCGGGCGGGCAGTAAAGCGCTGTTTGCAGCCCGTCTGGTGCAGGCGCCCCAGATAGCGGCCAACCCATTCCATCTGATCAAGGTTATCCGCTTCGAACTGACGACCGCCAAGGCTTGGGAAAACGGCAAAGTAGAATCCCTGATGCTGATGAAGCGTGCTGTCATTAAATAAGAGCGGCGCAGCAACGGGC\n\
GCCCGCGAAGCGGAGCTGGCCGCCTGCAAAGGCCGTTCGCGCTCGCTGTCGCTGGATCTGTACGCCCAGTGGCGCTGCATGGAGGACAACCACGGCAAGTGGCGCTTCACCTCGCCGACCCATACCGTGCTGGCCTTCGCCCAGGCGCTGAAAGAGCTGGCGCAGGAGGGCGGCGTCAGCGCTCGCCATCAGCGCTACCGCAACAATCAGCGCCGTCTGGTGGCAGGGATGCGCGCGCTCGGCTTCCGGCC\n\ +SRR1222430.3 3 length=236\n\
+SRR1222430.1 1 length=251\n\ CCCCCFFCFFFFGGGGGGGGGGHHHHHFGHHHHHHHHGGGGGHHHHHGGGGGGGGGGHHHHHHGGGGGHHHHHHHHGGGGHGHGHHGGHGGGGGGGGHHHHHGGGGGHGGGGHHHHGHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFABF\n\
CCCCCCCCCBBCGGCGGGGG@GGGGGHHHGHBHH@GGHGGGGGGGGG@GHGHGGGHHHHHHHHHGGGGGHHHFCGGGGHHHGHHGGHHHHGGGGCCGGGGHFFGGGGGHHHHHGGGGGGCGHHHHGGGGGGGGGGGGGGGGGGAEGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEDFFFFFFFFFFF:DA;CCFFBBFDAFFFAFFFFFFFFA-9A>DFFFFFBFFB\n\
@SRR1222430.2 2 length=250\n\ @SRR1222430.2 2 length=250\n\
AGAAATTCGCCATCAGAATAAAAACCTCATATGCACATTTTCTTGTTATTGCACAGCCTGTGCCACTTTAGCGCCAGCCTCTCCGGCAATCGTGGAGAAATTAAGGAGATAGTGTAATTTATCATGTTGCTTTTGCCGTATCGTAAAGAAACCTCGAGCTTTCCTGCCAGCAGGTAGCGAGTCTGCTTCGTCACCGCAGACCGGCGCATTATCCCTTGCCGGTGTGAAACCTCATTTCATTTAAGTCAAA\n\ AGAAATTCGCCATCAGAATAAAAACCTCATATGCACATTTTCTTGTTATTGCACAGCCTGTGCCACTTTAGCGCCAGCCTCTCCGGCAATCGTGGAGAAATTAAGGAGATAGTGTAATTTATCATGTTGCTTTTGCCGTATCGTAAAGAAACCTCGAGCTTTCCTGCCAGCAGGTAGCGAGTCTGCTTCGTCACCGCAGACCGGCGCATTATCCCTTGCCGGTGTGAAACCTCATTTCATTTAAGTCAAA\n\
+SRR1222430.2 2 length=250\n\ +SRR1222430.2 2 length=250\n\
BBBBBFFFBBBBFGGGGGGGGGHHGGHHHHHHHHGFGHHHHHHHHGHHHFFFHHFHHHHHHEHGFHHHFGFGFGGGEGGFH@@HGCGGGHHGHHGGHFAFHHHEGFHHGGHHFHFHHHHHEHHHHHHHHHHHGHHHGGGGHHGHFGGFDGFGFHGEGFCDHGGHHHHHHHGHHEHHGHGGGGHGFHHEHGHGGGGDFGGGHHGADA?DBGGGGGGFFFFBBFFFFFFFFFFFFFFFFFBFFFFFFFFF/B\n\ BBBBBFFFBBBBFGGGGGGGGGHHGGHHHHHHHHGFGHHHHHHHHGHHHFFFHHFHHHHHHEHGFHHHFGFGFGGGEGGFH@@HGCGGGHHGHHGGHFAFHHHEGFHHGGHHFHFHHHHHEHHHHHHHHHHHGHHHGGGGHHGHFGGFDGFGFHGEGFCDHGGHHHHHHHGHHEHHGHGGGGHGFHHEHGHGGGGDFGGGHHGADA?DBGGGGGGFFFFBBFFFFFFFFFFFFFFFFFBFFFFFFFFF/B\n\
@SRR1222430.3 3 length=236\n\ @SRR1222430.1 1 length=251\n\
CAAACACCTGACGCGGTTCCAGCAGGTACTCCTGCACGCCAATTTCCGGGCGGGCAGTAAAGCGCTGTTTGCAGCCCGTCTGGTGCAGGCGCCCCAGATAGCGGCCAACCCATTCCATCTGATCAAGGTTATCCGCTTCGAACTGACGACCGCCAAGGCTTGGGAAAACGGCAAAGTAGAATCCCTGATGCTGATGAAGCGTGCTGTCATTAAATAAGAGCGGCGCAGCAACGGGC\n\ GCCCGCGAAGCGGAGCTGGCCGCCTGCAAAGGCCGTTCGCGCTCGCTGTCGCTGGATCTGTACGCCCAGTGGCGCTGCATGGAGGACAACCACGGCAAGTGGCGCTTCACCTCGCCGACCCATACCGTGCTGGCCTTCGCCCAGGCGCTGAAAGAGCTGGCGCAGGAGGGCGGCGTCAGCGCTCGCCATCAGCGCTACCGCAACAATCAGCGCCGTCTGGTGGCAGGGATGCGCGCGCTCGGCTTCCGGCC\n\
+SRR1222430.3 3 length=236\n\ +SRR1222430.1 1 length=251\n\
CCCCCFFCFFFFGGGGGGGGGGHHHHHFGHHHHHHHHGGGGGHHHHHGGGGGGGGGGHHHHHHGGGGGHHHHHHHHGGGGHGHGHHGGHGGGGGGGGHHHHHGGGGGHGGGGHHHHGHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFABF\n\ CCCCCCCCCBBCGGCGGGGG@GGGGGHHHGHBHH@GGHGGGGGGGGG@GHGHGGGHHHHHHHHHGGGGGHHHFCGGGGHHHGHHGGHHHHGGGGCCGGGGHFFGGGGGHHHHHGGGGGGCGHHHHGGGGGGGGGGGGGGGGGGAEGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEDFFFFFFFFFFF:DA;CCFFBBFDAFFFAFFFFFFFFA-9A>DFFFFFBFFB\n\
"; ";
char expected_content_PE2[]="@SRR1222430.1 1 length=250\n\
CGATGCTGCGCTGCATCAATAAGCTGGAAGAGATCACCAGCGGCGATCTGATTGTCGATGGTCTGAAGGTCAACGACCCGAAGGTGGACGAACGTCTGATTCGTCAGGAAGCCGGGATGGTTTTCCAGCAGTTTTATCTGTTCCCGCACCTCACGGCGCTGGAAAACGTGATGTTTGGCCCGCTGCGGGTACGCGGCGCCAGCAAGCAGGCGGCGAGTGCAGGCTATCGTCGAGCAGCGGCCGGAAGCCG\n\ char expected_content_PE2[]="@SRR1222430.3 3 length=236\n\
+SRR1222430.1 1 length=250\n\ GCCCGTTGCTGCGCCGCTCTTATTTAATGACAGCACGCTTCATCAGCATCAGGGATTCTACTTTGCCGTTTTCCCAAGCCTTGGCGGTCGTCAGTTCGAAGCGGATAACCTTGATCAGATGGAATGGGTTGGCCGCTATCTGGGGCGCCTGCACCAGACGGGCTGCAAACAGCGCTTTACTGCCCGCCCGGAAATTGGCGTGCAGGAGTACCTGCTGGAACCGCGTCAGGTGTTTG\n\
CCCCCCFFFCCCGGGGGGGGGGHHHHHHHHGHHHHHHHHHHGGGGGGGGHHGHHHHGHGHGHHHHHHHHHFHHHGGGGGGGGGGBFFHHGGGGGGHHGGHHHGHGGGHHHHHHGGGGGGGFGHGHHHHHHHHHGHHHFHHHHHHDFGGGGHHHHHGGAGGGGGGGGGGGGGGGFGGGFFFFFFFFFFFA=@FDF-BFFFFFFFFFFFFFEDFBDFFF-:FFFFFF/BFFFEFFFFFFFFFFF;--:DEFF\n\ +SRR1222430.3 3 length=236\n\
?BBABBFBBFFFGGGGGGGGGGHHHHHHHHHHFHHHGGGGGHHHHHHHGHHHHHGHGHHHHHHHGHFEGGHGHHHHHHGGHHHHHGGGEGGGHGHHHGHHGGCGGGDHHHHHHHHGHHGHGHHHHHHFHGGGHFGGGGGHHHHEFGGCFGHHHHGGFGGGGGGGGGGGGGGGGGFFFEFFFFFFFBFFFFF=;ABFF/FA:DB;BF.9.BFFFFFFF/AFFFFFABDFFB/9BD.;\n\
@SRR1222430.2 2 length=251\n\ @SRR1222430.2 2 length=251\n\
AGAAATTCGCCAGGGTGATCAACGTCTCATCGTCGGCGAGGGTCAGCGCCTGCGCGGGACAGTTTTCCACACAGGCCGGCCCCGCCTCGCGGCCCTGGCATAGATCGCACTTGTGCGCGCTGGCTTTCACCAGGCCTGCGGCCTGCGGCGTCACCACCACCTGCATCACCCCGAACGGGCAGGCCACCATGCAGGATTTACAGCCAATGCATTTCTCCTGACGGACCTGAACGCTGTCGCCGGACTGGGCG\n\ AGAAATTCGCCAGGGTGATCAACGTCTCATCGTCGGCGAGGGTCAGCGCCTGCGCGGGACAGTTTTCCACACAGGCCGGCCCCGCCTCGCGGCCCTGGCATAGATCGCACTTGTGCGCGCTGGCTTTCACCAGGCCTGCGGCCTGCGGCGTCACCACCACCTGCATCACCCCGAACGGGCAGGCCACCATGCAGGATTTACAGCCAATGCATTTCTCCTGACGGACCTGAACGCTGTCGCCGGACTGGGCG\n\
+SRR1222430.2 2 length=251\n\ +SRR1222430.2 2 length=251\n\
>1>AAFFF@11AEGGFFCGGGGGFGHFH2FF1F00EEE/@AEE0FGGFGEGGHGGCGC?EEFHEFEEHDF1EECHEFE/@@/BCCCFGAC@CC@C.CEGFHFHGHFHCEC?FH;CC?CG@@?-AF.BB0BFGF?E./EF;@?;AFF@<-@@??BFF?F-:A?BF999BBBF@@?@@@F-;@B@FF-A-9FF/BFFE/F//B/BBEFBFFFFF/BFFFFFFFEB?-@=B-/BBF--:;/A-B>--;>?EFE9\n\ >1>AAFFF@11AEGGFFCGGGGGFGHFH2FF1F00EEE/@AEE0FGGFGEGGHGGCGC?EEFHEFEEHDF1EECHEFE/@@/BCCCFGAC@CC@C.CEGFHFHGHFHCEC?FH;CC?CG@@?-AF.BB0BFGF?E./EF;@?;AFF@<-@@??BFF?F-:A?BF999BBBF@@?@@@F-;@B@FF-A-9FF/BFFE/F//B/BBEFBFFFFF/BFFFFFFFEB?-@=B-/BBF--:;/A-B>--;>?EFE9\n\
@SRR1222430.3 3 length=236\n\ @SRR1222430.1 1 length=250\n\
GCCCGTTGCTGCGCCGCTCTTATTTAATGACAGCACGCTTCATCAGCATCAGGGATTCTACTTTGCCGTTTTCCCAAGCCTTGGCGGTCGTCAGTTCGAAGCGGATAACCTTGATCAGATGGAATGGGTTGGCCGCTATCTGGGGCGCCTGCACCAGACGGGCTGCAAACAGCGCTTTACTGCCCGCCCGGAAATTGGCGTGCAGGAGTACCTGCTGGAACCGCGTCAGGTGTTTG\n\ CGATGCTGCGCTGCATCAATAAGCTGGAAGAGATCACCAGCGGCGATCTGATTGTCGATGGTCTGAAGGTCAACGACCCGAAGGTGGACGAACGTCTGATTCGTCAGGAAGCCGGGATGGTTTTCCAGCAGTTTTATCTGTTCCCGCACCTCACGGCGCTGGAAAACGTGATGTTTGGCCCGCTGCGGGTACGCGGCGCCAGCAAGCAGGCGGCGAGTGCAGGCTATCGTCGAGCAGCGGCCGGAAGCCG\n\
+SRR1222430.3 3 length=236\n\ +SRR1222430.1 1 length=250\n\
?BBABBFBBFFFGGGGGGGGGGHHHHHHHHHHFHHHGGGGGHHHHHHHGHHHHHGHGHHHHHHHGHFEGGHGHHHHHHGGHHHHHGGGEGGGHGHHHGHHGGCGGGDHHHHHHHHGHHGHGHHHHHHFHGGGHFGGGGGHHHHEFGGCFGHHHHGGFGGGGGGGGGGGGGGGGGFFFEFFFFFFFBFFFFF=;ABFF/FA:DB;BF.9.BFFFFFFF/AFFFFFABDFFB/9BD.;\n\ CCCCCCFFFCCCGGGGGGGGGGHHHHHHHHGHHHHHHHHHHGGGGGGGGHHGHHHHGHGHGHHHHHHHHHFHHHGGGGGGGGGGBFFHHGGGGGGHHGGHHHGHGGGHHHHHHGGGGGGGFGHGHHHHHHHHHGHHHFHHHHHHDFGGGGHHHHHGGAGGGGGGGGGGGGGGGFGGGFFFFFFFFFFFA=@FDF-BFFFFFFFFFFFFFEDFBDFFF-:FFFFFF/BFFFEFFFFFFFFFFF;--:DEFF\n\
"; ";
void test_write_PE() { void test_write_PE() {
srp sr; srp sr;
srp::reverse_iterator rit; srp::reverse_iterator rit;
......
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