Fix changing number of fields by SeqFilter

.travis.yml

@@ -6,6 +6,15 @@ perl:
   - "5.18.3-thr"
   - "5.20.1-thr"
   - "5.22.0-thr"
+env:
+    - SAMTOOLSVERSION="1.2"
+    - SAMTOOLSVERSION="1.3"
+    - SAMTOOLSVERSION="1.3.1"
+    - SAMTOOLSVERSION="1.4"
+    - SAMTOOLSVERSION="1.4.1"
+    - SAMTOOLSVERSION="1.5"
+    - SAMTOOLSVERSION="1.6"
+    - SAMTOOLSVERSION="1.7"
 cache:
   directories:
     - $HOME/samtools-$SAMTOOLSVERSION
@@ -15,9 +24,6 @@ addons:
   apt:
     packages:
     - ncbi-blast+
-env:
-    - SAMTOOLSVERSION="1.3"
-    - SAMTOOLSVERSION="1.2"
 before_install:
   - git clone git://github.com/travis-perl/helpers ~/travis-perl-helpers
   - source ~/travis-perl-helpers/init
@@ -29,8 +35,9 @@ install:
     - cd $HOME && wget 'https://github.com/samtools/samtools/releases/download/'"$SAMTOOLSVERSION"'/samtools-'"$SAMTOOLSVERSION"'.tar.bz2'
     - tar xjf samtools-"$SAMTOOLSVERSION".tar.bz2
     - cd samtools-"$SAMTOOLSVERSION" && make && export PATH=$PWD:"$PATH" && ls && pwd && cd -
+    - mkdir -p /tmp/shunit2 && cd /tmp/shunit2 && wget 'https://github.com/greatfireball/shunit2/archive/v2.1.7.tar.gz' -O - | tar xzf - --strip 1
 script: 
-    - cd $PROOVREADDIR && make sample
+    - cd $PROOVREADDIR/test && bash testInstallation.sh && bash testSeqFilterError.sh
 notifications:
     slack:
         secure: Mu7v0562KyuYMc76eg+9UWtqdF25fH9+ZKBzDD19h41YkjzxCmdPvF+jyD0SJGTsMZh0lKXSt8Ftqb9EWk3JDqzrkNOsDQunNuFwOgT/kF9i0s69mYl7KYR8vUUFHZirJ2aEXrWkeM1kF/tcopmMp/YytALKDDSoW1/6jHRj/go=

bin/proovread

@@ -1708,14 +1708,15 @@ sub correct_sr_mt{
         $VB->hline;
         $VB->verbose($cmd);
         my $re = qx($cmd);
-        my ($bpt, $bpN) = (split(/\s/, $re))[1,6];
+	# extract the second field (total number of nucleotids) and the last field (number of N positions)
+        my ($bpt, $bpN) = (split(/\s/, $re))[1,-1];
         $VB->hline;
 
         $V->exit("SeqFilter failed to mask $fq_file: $?\n") if $?;
 
         my $bpN_frac = $bpN/$bpt;
         $VB->nline;
-        $VS->verbose(sprintf "Masked : %0.1f%%", $bpN/$bpt*100);
+        $VS->verbose(sprintf "Masked : %0.1f%%", $bpN_frac*100);
 
 	return wantarray ? (\@ref_idxs, $bpN_frac) : \@ref_idxs; # wantarray guarantees backward compatibility
 }

sample/F.antasticus_long_error.singleseq.fq

@@ -0,0 +1,4 @@
+@long_error_0_0 RSTART:86026 with-iupac-chars
+GAGTGAAAAAGTGACGGCGCTAGGATTAAACGTGGTGCAATGACAMTCGGATGGCATAACGCGTCTGCTTGCGGGCAGTGGAAGTCATCCCCCGTCTCCTTTGGGTTATATTATACACCCGGAAAAAGTTCGCCTTTGAGAACCCAACGCCAAAGATCTAGACGCGGACAAATCAGGACACCCCCGTCTAAACGTGACGCTCATTGCACAACCAAAATGAATTGGGCAGTCAGTATAAGGCGGTCAAATTGACTATCTTAGCCTGTTATGTAGTCGAGTGAGGTTTTACACAGCTCTTACCGATGGTTAAATAACCGTATTGTCGTTTCTGCATGTACTGCTTGGAACGCAGGGGAGTTTCTCAATGCGTCCATAATCTTCGGTTGGGTACCAGTGTGACCTGTAGCAGAACATCGCGCCAGAGCTGGCAGGACAGGAAGAACCGCATTAGCGGCCACTTTTACTTCAAACGCCATCTTAATTAGCCTTATTGTCCGTTGGCGATCTGCCCGCAAGGACCGCTTCCGTACTTATAAGGTTGCAGAATCGATGTGAGATTTTTAGTTGTCCCTCTTCGACTTCCGTTTTCATACAGTGAAATGTTAAGGGTTTAGATGTACAACGGGCTTTCTTGTCTAGGAGAGACCGTTGCGGCGTGCAACCCCGAGTAAGCACGGATATGGGGCATTTCGTCCCTGAGTACTGGTAGTGAGCTGGGCCGACCATCGGTAGGGGGCCGGCGGAGCTCGCCTATGCGGGTCCCTGCTTGTGTAAGCCCCAAGGATCTTACTAAGTTCCTGCCGTGTTCTAGGCCCGGGATAGGATTAGTGAGTCCTCAGCTCTACCTGACGTTGGCGACGGCCAAGTTACTTATGTACTCCCATCCCATTCGCGGTGCCTTCGATACAGGTAGAACCGTTTATACTACGAGGTGTGCTTCACGGCTAACTTATCCGGTGCGTACATCTCTGGATAGACTTTGGATCTGTACTGTGATACTCTCTCCTGTACGCTACATCTGAACCTCTGGTAATCCTCGTCTGCGCTTCAAG
++
+$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

test/testInstallation.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+testInstallation() {
+    ../bin/proovread --pre test --overwrite --long ../sample/F.antasticus_long_error.fq --short ../sample/F.antasticus_short.fq --sr-qv-offset 33 &>/dev/null
+    returnCode=$?
+    assertEquals "Testrun exited with exit code of 0" 0 $returnCode
+    assertTrue "test.trimmed.fq exists" "[ -e test/test.trimmed.fq ]"
+    assertTrue "test.trimmed.fa exists" "[ -e test/test.trimmed.fa ]"
+    assertTrue "test.untrimmed.fq exists" "[ -e test/test.untrimmed.fq ]"
+}
+
+. /tmp/shunit2/shunit2

test/testSeqFilterError.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+testMultipleSeqs() {
+    ../bin/proovread --pre test_multiple_seqs --overwrite --long ../sample/F.antasticus_long_error.fq --short ../sample/F.antasticus_short.fq --sr-qv-offset 33 2>log_multiple_seqs
+    returnCode=$?
+    assertEquals "Testrun exited with exit code of 0" 0 $returnCode
+    numWarnings=$(grep -c "Use of uninitialized value \$bpN in division" log_multiple_seqs)
+    assertEquals "No warnings messages are given indicating a problem with SeqFilter" 0 $numWarnings
+}
+
+testSingleSeq() {
+    ../bin/proovread --pre test_single_seq --overwrite --long ../sample/F.antasticus_long_error.singleseq.fq --short ../sample/F.antasticus_short.fq --sr-qv-offset 33 2>log_single_seq
+    returnCode=$?
+    assertEquals "Testrun exited with exit code of 0" 0 $returnCode
+    numWarnings=$(grep -c "Use of uninitialized value \$bpN in division" log_single_seq)
+    assertEquals "No warnings messages are given indicating a problem with SeqFilter" 0 $numWarnings
+}
+
+. /tmp/shunit2/shunit2