samtools rmdup removes single read from pair

[mfz]

samtools rmdup removes single read from a pair when 2 pairs with same position for all 4 reads are present

i.e. input file

WPHISEQ06:99:C6L3PANXX:5:1101:1124:56798_1:N:0: 163 chr2 175312986 42 34M = 175312986 -34
WPHISEQ06:99:C6L3PANXX:5:1101:13415:91660_1:N:0: 163 chr2 175312986 23 34M = 175312986 -34
WPHISEQ06:99:C6L3PANXX:5:1101:1124:56798_1:N:0: 83 chr2 175312986 42 34M = 175312986 34
WPHISEQ06:99:C6L3PANXX:5:1101:13415:91660_1:N:0: 83 chr2 175312986 23 34M = 175312986 34

output after samtools rmdup

WPHISEQ06:99:C6L3PANXX:5:1101:1124:56798_1:N:0: 163 chr2 175312986 42 34M = 175312986 -34
WPHISEQ06:99:C6L3PANXX:5:1101:13415:91660_1:N:0: 163 chr2 175312986 23 34M = 175312986 -34
WPHISEQ06:99:C6L3PANXX:5:1101:13415:91660_1:N:0: 83 chr2 175312986 23 34M = 175312986 34

samtools git version 1.2-242-g4d56437
htslib git version 1.2.1-256-ga356746

Example file to reproduce error
test.sam.txt

[kirkmcclure]

The rmdup logic assumes that the QNAME fields are identical for duplicates.
After manually changing QNAME for the second pair in the example -

./samtools view -b /tmp/Issue497.sam |./samtools sort -n -o - - |./samtools rmdup - - |./samtools view -h - |tail
[bam_rmdup_core] processing reference chr2...
[bam_rmdup_core] 1 / 2 = 0.5000 in library '    '
@SQ SN:chrUn_KI270757v1 LN:71251
@SQ SN:chrUn_GL000214v1 LN:137718
@SQ SN:chrUn_KI270742v1 LN:186739
@SQ SN:chrUn_GL000216v2 LN:176608
@SQ SN:chrUn_GL000218v1 LN:161147
@SQ SN:chrX LN:156040895
@SQ SN:chrY LN:57227415
@SQ SN:chrY_KI270740v1_random   LN:37240
WPHISEQ06:99:C6L3PANXX:5:1101:1124:56798_1:N:0: 163 chr2    1753129 86  23  34M =   175312986   -34 ATACAAAAATTTACCGCTTTACTAATAATCCACT  ;?B1DFEGGFGGG11?/<=<FGGGGGGGGGGGGG
WPHISEQ06:99:C6L3PANXX:5:1101:1124:56798_1:N:0: 83  chr2    1753129 86  23  34M =   175312986   34  ATACAAAAATTTACCGCTTGACTAATAATCCACT  GGGGB:1GGF=E=;/1GF=1BEF;1>11GB@A3B

[jrandall]

Confirmed that the provided test file still exhibits this issue with current samtools/htslib ("1.3-5-g664cc5f (using htslib 1.3-5-gdf4a80e)").

[whitwham]

As rmdup is deprecated and nobody has touched this for two years I am going to close this issue.