seqtk mergepe produces invalid FASTQ output on empty input sequences #109
Description
When one of the sequences to merge is empty (has zero length), mergepe produces output which isn't a valid FASTQ file. Example:
1.fq
@D00723:158:CAJ17ANXX:6:1103:3343:29327 1:N:0:GAGATTCC+CCTATCCT
GTGGGCACCTGTCATCCCAGCTACTTGGGAGGCTGAGTCAGGAGAATCACTGGAACCTAGGAGTTGGAGTTTGTAGTGAGCCAAGATCGCACCACTGCACTCCAGCCTGGGCGACAGAATGAGAC
+
</<<B<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFBF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF<FBFFFFF<
@D00723:158:CAJ17ANXX:6:1103:3362:29333 1:N:0:GAGATTCC+CCTATCCT
GGAAGGGGAAAGACAAGAAAGAGGGAGACGGAGAGAGAGAGAGAAGGAAAAGGAAGGATGACAAGACAGGAAGACAGAGAAAAGAAAAAGACTGAAGGAGGGAAGGAAGGAAAGAAGGGAAGG
+
B/<<BFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFBFFFFFFFFF/FFFFBFFFFFFFFFF<
@D00723:158:CAJ17ANXX:6:1103:3606:29320 1:N:0:GAGATTCC+CCTATCCT
GGCCCACTCTGTCTGGCTCCCAACTTCCCTTTGAGGCTTCCCGGTCCTGGGGTAACAGCTGGCTTAGGGGAGCCAGTCGGGGCTGCCTTCCAGGCTTCCAGGTCCACTTTAAGGAGGGATGGGG
+
B<BBBFFFFFFFFFFFFFFFFBFFFFFFFFFFBB/<BFFFFFFFBFFFFFFFBFFF//FFFFFFFFFF/BFFFBFFFFBFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFF7/B<<FFFFFB
2.fq
@D00723:158:CAJ17ANXX:6:1103:3343:29327 2:N:0:GAGATTCC+CCTATCCT
GTTGTGCAGCCCTCAGCGCCACCCACCACCAGAACTCTCCCCACCTTTGACGCACGTGTGCAGAACTGAAGGCCACGCTGGAATTGTAGCCCACGTGCCACACTGCTGGCTGTGTCATGGATATC
+
BBBBBFFFFFFFFFFFFFFBFFFFFFFBFFFFFFFFFFFFFF/FFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF<B//B<FFFFFFFFFFFFFFFFBFFFFF/BB/F/B/B7/<FFFFF<
@D00723:158:CAJ17ANXX:6:1103:3362:29333 2:N:0:GAGATTCC+CCTATCCT
+
@D00723:158:CAJ17ANXX:6:1103:3606:29320 2:N:0:GAGATTCC+CCTATCCT
GAGGACCAGCAGCTGGACATCCAGGTCATGGCAGAGGCCAGAGAGTCCTGGGACCTGGGCCTACAGGAGCAGGAGGGGCGGTACACACCTCTGCCCTTGGGCGGGAACAAGGAGCAAGCCATCT
+
/BBBBFFFFFFFFFFBFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFF<FFFFFBFFFFBFFFFFFFFFF<FFBFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFBBFFFFFFFF<FFFFFFB/
Output of seqtk mergepe 1.fq 2.fq
@D00723:158:CAJ17ANXX:6:1103:3343:29327 1:N:0:GAGATTCC+CCTATCCT
GTGGGCACCTGTCATCCCAGCTACTTGGGAGGCTGAGTCAGGAGAATCACTGGAACCTAGGAGTTGGAGTTTGTAGTGAGCCAAGATCGCACCACTGCACTCCAGCCTGGGCGACAGAATGAGAC
+
</<<B<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFBF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF<FBFFFFF<
@D00723:158:CAJ17ANXX:6:1103:3343:29327 2:N:0:GAGATTCC+CCTATCCT
GTTGTGCAGCCCTCAGCGCCACCCACCACCAGAACTCTCCCCACCTTTGACGCACGTGTGCAGAACTGAAGGCCACGCTGGAATTGTAGCCCACGTGCCACACTGCTGGCTGTGTCATGGATATC
+
BBBBBFFFFFFFFFFFFFFBFFFFFFFBFFFFFFFFFFFFFF/FFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF<B//B<FFFFFFFFFFFFFFFFBFFFFF/BB/F/B/B7/<FFFFF<
@D00723:158:CAJ17ANXX:6:1103:3362:29333 1:N:0:GAGATTCC+CCTATCCT
GGAAGGGGAAAGACAAGAAAGAGGGAGACGGAGAGAGAGAGAGAAGGAAAAGGAAGGATGACAAGACAGGAAGACAGAGAAAAGAAAAAGACTGAAGGAGGGAAGGAAGGAAAGAAGGGAAGG
+
B/<<BFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFBFFFFFFFFF/FFFFBFFFFFFFFFF<
>D00723:158:CAJ17ANXX:6:1103:3362:29333 2:N:0:GAGATTCC+CCTATCCT
@D00723:158:CAJ17ANXX:6:1103:3606:29320 1:N:0:GAGATTCC+CCTATCCT
GGCCCACTCTGTCTGGCTCCCAACTTCCCTTTGAGGCTTCCCGGTCCTGGGGTAACAGCTGGCTTAGGGGAGCCAGTCGGGGCTGCCTTCCAGGCTTCCAGGTCCACTTTAAGGAGGGATGGGG
+
B<BBBFFFFFFFFFFFFFFFFBFFFFFFFFFFBB/<BFFFFFFFBFFFFFFFBFFF//FFFFFFFFFF/BFFFBFFFFBFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFF7/B<<FFFFFB
@D00723:158:CAJ17ANXX:6:1103:3606:29320 2:N:0:GAGATTCC+CCTATCCT
GAGGACCAGCAGCTGGACATCCAGGTCATGGCAGAGGCCAGAGAGTCCTGGGACCTGGGCCTACAGGAGCAGGAGGGGCGGTACACACCTCTGCCCTTGGGCGGGAACAAGGAGCAAGCCATCT
+
/BBBBFFFFFFFFFFBFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFF<FFFFFBFFFFBFFFFFFFFFF<FFBFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFBBFFFFFFFF<FFFFFFB/
Note how @D00723:158:CAJ17ANXX:6:1103:3362:29333 2:N:0:GAGATTCC+CCTATCCT from the second file was transformed into >D00723:158:CAJ17ANXX:6:1103:3362:29333 2:N:0:GAGATTCC+CCTATCCT in the output.