Changeset: e73718a4b2fe for MonetDB URL: https://dev.monetdb.org/hg/MonetDB/rev/e73718a4b2fe Modified Files: ChangeLog sql/backends/monet5/vaults/sambam/sambam.c sql/test/file_loader/sambam/Tests/read_file1.bam.test.in sql/test/file_loader/sambam/Tests/read_file1.sam.test.in Branch: samloader Log Message:
Improve sam/bam reader. It now uses a tab as separator for the sam_aux data, similar to what is used in a sam file. Added info on the minimum supported HTSlib version in Changelog. Updated and extended tests. diffs (truncated from 391 to 300 lines): diff --git a/ChangeLog b/ChangeLog --- a/ChangeLog +++ b/ChangeLog @@ -11,6 +11,7 @@ We use the HTSlib for reading these files and the library needs to be pre-installed on your OS (e.g. on Fedora via: sudo dnf install htslib). See also: https://www.htslib.org/download/ + The HTSlib must be version 1.24 or higher. Also the MonetDB server has to be started with startup argument: --loadmodule htslib to enable it. By default it is not enabled. diff --git a/sql/backends/monet5/vaults/sambam/sambam.c b/sql/backends/monet5/vaults/sambam/sambam.c --- a/sql/backends/monet5/vaults/sambam/sambam.c +++ b/sql/backends/monet5/vaults/sambam/sambam.c @@ -187,7 +187,7 @@ sam_query(int caller, mvc *sql, sql_subf /* TODO sam_open() logs error msg to stderr when it fails: [E::hts_open_format] Failed to open file "file1.sam" : No such file or directory */ - errmsg = "Could not open sam/bam file"; + errmsg = "Failed to open sam/bam file"; /* errmsg = RUNTIME_FILE_NOT_FOUND; */ goto end; } @@ -269,10 +269,10 @@ sam_query(int caller, mvc *sql, sql_subf BAT * b = bat_create(battype, estimate); if (b) { colmetadata[col].bat = b; - TRC_DEBUG(LOADER, "Created bat %d type %d size %lu\n", col+1, battype, estimate); + TRC_DEBUG(LOADER, "Created bat %d type %d size " BUNFMT "\n", col+1, battype, estimate); } else { errmsg = "Failed to create bat."; - TRC_ERROR(LOADER, "Failed to create bat %d type %d size %lu\n", col+1, battype, estimate); + TRC_ERROR(LOADER, "Failed to create bat %d type %d size " BUNFMT "\n", col+1, battype, estimate); /* cleanup already created bats */ while (col > 0) { col--; @@ -381,7 +381,7 @@ sam_query(int caller, mvc *sql, sql_subf while (aux && (pos < sizeof(buf))) { char aux_type = bam_aux_type(aux); if (pos > 0) - buf[pos++] = ' '; // add a separator between multiple TAG:TYPE:VALUE + buf[pos++] = '\t'; // add a tab separator between multiple TAG:TYPE:VALUE pos += snprintf(buf + pos, sizeof(buf) - pos, "%.2s:%c:", bam_aux_tag(aux), NULL != strchr("cCsSiI", aux_type) ? 'i' : aux_type); pos += printauxdata(buf + pos, sizeof(buf) - pos, aux_type, -1, aux); aux = bam_aux_next(bamdata, aux); @@ -401,7 +401,6 @@ sam_query(int caller, mvc *sql, sql_subf for (col = 0; col < SAM_NR_COLS; col++) { BAT * b = colmetadata[col].bat; BATsettrivprop(b); - /* TODO check that nil and nonil are set correctly for first 11 mandatory cols */ assert(BATcount(b) == (BUN)row); } diff --git a/sql/test/file_loader/sambam/Tests/read_file1.bam.test.in b/sql/test/file_loader/sambam/Tests/read_file1.bam.test.in --- a/sql/test/file_loader/sambam/Tests/read_file1.bam.test.in +++ b/sql/test/file_loader/sambam/Tests/read_file1.bam.test.in @@ -1,6 +1,6 @@ -- test reading file: file1.bam -statement error 42000!SELECT: file_loader function failed 'Could not open sam/bam file' +statement error 42000!SELECT: file_loader function failed 'Failed to open sam/bam file' SELECT count(*) FROM file_loader('file1.bam') statement error 42000!SELECT: file_loader function failed 'Filename extension missing' @@ -16,7 +16,7 @@ SELECT count(*) FROM r'$TSTSRCDIR/file1. ---- 71 -statement error 42000!SELECT: file_loader function failed 'Could not open sam/bam file' +statement error 42000!SELECT: file_loader function failed 'Failed to open sam/bam file' SELECT count(*) FROM 'file1.bam' query I nosort @@ -334,62 +334,62 @@ GGGF:GFGG?EGFEG?DAFBEF=FA+>EGG=E:EDBEB7D query T nosort SELECT DISTINCT SAM_AUX FROM r'$QTSTSRCDIR/file1.bam' ORDER BY 1 ---- -AS:i:0 YM:i:0 YP:f:0.5 -AS:i:0 YM:i:0 YP:f:0.99998 -AS:i:0 YM:i:0 YP:f:0.99999 -AS:i:0 YM:i:0 YP:f:0.999999 -AS:i:0 YM:i:0 YP:f:1 -AS:i:11 YM:i:11 YP:f:1 -AS:i:13 YM:i:13 YP:f:1 -AS:i:15 YM:i:15 YP:f:0.999998 -AS:i:16 YM:i:16 YP:f:0.99995 -AS:i:18 YM:i:18 YP:f:1 -AS:i:19 YM:i:19 YP:f:1 -AS:i:2 YM:i:2 YP:f:0.999997 -AS:i:2 YM:i:2 YP:f:1 -AS:i:21 YM:i:21 YP:f:1 -AS:i:22 YM:i:22 YP:f:1 -AS:i:29 YM:i:29 YP:f:1 -AS:i:30 YM:i:30 YP:f:1 -AS:i:33 YM:i:33 YP:f:0.984368 -AS:i:34 YM:i:34 YP:f:0.998418 -AS:i:34 YM:i:9 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+AS:i:85@YM:i:0@YA:Z:85,0,1=1I1=1I9=15D87=;85,0,1=1I1=1I8=15D88=;85,0,1=1I1=1I7=15D89=;85,0,1=1I1=1I6=15D90=;85,0,1=1I1=1I5=15D91=;85,0,1=1I1=1I4=15D92=;114,59,1=2X1I1X3=14D92=@YP:f:3.16228e-09 +AS:i:9@YM:i:9@YP:f:0.996848 +AS:i:91@YM:i:36@YA:Z:91,36,14=1X76=1056D2=1X2=1D4=;92,37,14=1X77=1058D1I1=1X5=;92,37,14=1X76=1058D1=1I1=1X5=;92,37,14=1X75=1058D2=1I1=1X5=;92,37,14=1X74=1058D3=1I1=1X5=;92,37,14=1X73=1058D4=1I1=1X5=;92,37,14=1X72=1058D5=1I1=1X5=;92,37,14=1X71=1058D6=1I1=1X5=;92,37,14=1X70=1058D7=1I1=1X5=;94,69,14=1X77=1057D1X1=1X5=@YP:f:1.25893e-09 +AS:i:92@YM:i:37@YA:Z:92,37,3=1I1=1X12=171D82=;92,37,3=1I1=1X11=171D83=;92,37,3=1I1=1X10=171D84=;92,37,3=1I1=1X9=171D85=;92,37,3=1I1=1X8=171D86=;92,37,3=1I1=1X7=171D87=;92,37,3=1I1=1X6=171D88=;92,37,3=1I1=1X5=171D89=;92,37,3=1I1=1X4=171D90=;92,37,3=1I1=1X3=171D91=;92,37,3=1I1=1X2=171D92=@YP:f:6.30957e-10 +AS:i:92@YM:i:37@YA:Z:92,37,3=1I1=1X13=1751D81=;92,37,3=1I1=1X12=1751D82=;92,37,3=1I1=1X11=1751D83=;92,37,3=1I1=1X10=1751D84=;92,37,3=1I1=1X9=1751D85=;92,37,3=1I1=1X8=1751D86=;92,37,3=1I1=1X7=1751D87=;92,37,3=1I1=1X6=1751D88=;92,37,3=1I1=1X5=1751D89=;92,37,3=1I1=1X4=1751D90=;92,37,3=1I1=1X3=1751D91=;92,37,3=1I1=1X2=1751D92=@YP:f:6.30957e-10 +AS:i:94@YM:i:94@YP:f:1 +AS:i:95@YM:i:95@YP:f:3.16224e-10 +AS:i:99@YM:i:99@YP:f:1.25891e-10 statement error 42000!SELECT: identifier 'SAM_RGAUX' unknown SELECT DISTINCT SAM_RGAUX FROM r'$QTSTSRCDIR/file1.bam' ORDER BY 1 @@ -408,11 +408,26 @@ chr13 0 TATACTTATAGAACAAATGAACCCAAAACCACATAAGGTAAACAACAAAGCTACTGGTTCAAAATTAAGCCTAACTTCAACAGTACCAGGCAAAAACCAT CGF?BB;DAEFEEEGEFGE@5EABGD/>DGDDB@5EA@B=EDEDGC?CE5B3GBAED5D?GEB>D?-EC@##?:DBDA3#2G:@E#F>A5D####A#A## -AS:i:95 YM:i:95 YP:f:3.16224e-10 - --- AS:i:95 YM:i:95 YP:f:3.16224e-10 +AS:i:95@YM:i:95@YP:f:3.16224e-10 query TITIITTIITTT nosort SELECT * FROM r'$QTSTSRCDIR/file1.bam' LIMIT 0 ---- +query TITIITTIITTT nosort +SELECT qname,flag,rname,pos,mapq,cigar,rnext,pnext,tlen,seq,qual,sam_aux +FROM r'$QTSTSRCDIR/file1.bam' OFFSET 2 ROWS FETCH FIRST 1 ROW ONLY +---- +sim_22_1_a +339 +chr14 +18226024 +0 +100= +chr14 +4 +0 +GTACAAAAGTGGGAAATTTTAAAGCTGGGCATCCAGGGGAGACATCACGTGTCAGTAGGTTCCGTGATGCCCCCCAAGCCGCAAAACCAGCAAGTTTTTA +####F#EFCGEC5BE?EF#F=@?DF658;DEDG=@FBG@?E=DE=F#FDB?CCGE1GFFEDEFFDGGFE>FFCGEGGG:;B@FFG@DDGGGFGB7FBC?F +AS:i:0@YM:i:0@YP:f:0.5 + diff --git a/sql/test/file_loader/sambam/Tests/read_file1.sam.test.in b/sql/test/file_loader/sambam/Tests/read_file1.sam.test.in --- a/sql/test/file_loader/sambam/Tests/read_file1.sam.test.in +++ b/sql/test/file_loader/sambam/Tests/read_file1.sam.test.in @@ -1,6 +1,6 @@ -- test reading file: file1.sam -statement error 42000!SELECT: file_loader function failed 'Could not open sam/bam file' +statement error 42000!SELECT: file_loader function failed 'Failed to open sam/bam file' SELECT count(*) FROM file_loader('file1.sam') statement error 42000!SELECT: file_loader function failed 'Filename extension missing' @@ -16,7 +16,7 @@ SELECT count(*) FROM r'$TSTSRCDIR/file1. ---- 71 -statement error 42000!SELECT: file_loader function failed 'Could not open sam/bam file' +statement error 42000!SELECT: file_loader function failed 'Failed to open sam/bam file' SELECT count(*) FROM 'file1.sam' query I nosort @@ -334,62 +334,62 @@ GGGF:GFGG?EGFEG?DAFBEF=FA+>EGG=E:EDBEB7D query T nosort SELECT DISTINCT SAM_AUX FROM r'$QTSTSRCDIR/file1.sam' ORDER BY 1 ---- -AS:i:0 YM:i:0 YP:f:0.5 -AS:i:0 YM:i:0 YP:f:0.99998 -AS:i:0 YM:i:0 YP:f:0.99999 -AS:i:0 YM:i:0 YP:f:0.999999 -AS:i:0 YM:i:0 YP:f:1 -AS:i:11 YM:i:11 YP:f:1 -AS:i:13 YM:i:13 YP:f:1 -AS:i:15 YM:i:15 YP:f:0.999998 -AS:i:16 YM:i:16 YP:f:0.99995 -AS:i:18 YM:i:18 YP:f:1 -AS:i:19 YM:i:19 YP:f:1 -AS:i:2 YM:i:2 YP:f:0.999997 -AS:i:2 YM:i:2 YP:f:1 -AS:i:21 YM:i:21 YP:f:1 -AS:i:22 YM:i:22 YP:f:1 -AS:i:29 YM:i:29 YP:f:1 -AS:i:30 YM:i:30 YP:f:1 -AS:i:33 YM:i:33 YP:f:0.984368 -AS:i:34 YM:i:34 YP:f:0.998418 -AS:i:34 YM:i:9 YA:Z:34,9,10=1368D52=1X37=;34,9,9=1368D53=1X37=;34,9,8=1368D54=1X37= YP:f:0.00315231 -AS:i:36 YM:i:36 YP:f:0.996035 -AS:i:39 YM:i:39 YP:f:0.999968 -AS:i:4 YM:i:4 YP:f:0.999749 -AS:i:40 YM:i:40 YP:f:0.000251126 -AS:i:47 YM:i:22 YA:Z:47,22,91=172D7=1X1=;49,24,90=172D1X7=1X1=;49,24,89=172D1=1X7=1X1=;49,24,88=172D2=1X7=1X1=;49,24,87=172D3=1X7=1X1=;49,24,86=172D4=1X7=1X1=;49,24,85=172D5=1X7=1X1= YP:f:1.99522e-05 -AS:i:49 YM:i:49 YP:f:0.998009 -AS:i:51 YM:i:21 YP:f:0.0156012 -AS:i:52 YM:i:52 YP:f:1 -AS:i:53 YM:i:53 YP:f:5.01182e-06 -AS:i:57 YM:i:2 YA:Z:57,2,2=1D8=617D10=1X79=;57,2,2=1D7=617D11=1X79=;57,2,2=1D6=617D12=1X79=;59,4,2=1D9=1X3=617D5=1X79=;59,4,2=1D9=1X2=617D6=1X79=;59,4,2=1D9=1X1=617D7=1X79=;59,4,2=1D9=1X617D8=1X79=;67,42,2=2X3=1X618D12=1X79= YP:f:3.16227e-06 -AS:i:57 YM:i:57 YP:f:1 -AS:i:59 YM:i:4 YA:Z:71,16,5=1I2=232D1X71=1X12=1X6= YP:f:5.01162e-05 -AS:i:6 YM:i:6 YP:f:0.999997 -AS:i:6 YM:i:6 YP:f:1 -AS:i:60 YM:i:0 YP:f:0.00396529 -AS:i:61 YM:i:6 YA:Z:61,6,1=1I11=72I4=1X5=1X4=;61,6,1=1I10=72I5=1X5=1X4=;61,6,1=1I9=72I6=1X5=1X4=;61,6,1=1I8=72I7=1X5=1X4=;61,6,1=1I7=72I8=1X5=1X4=;61,6,1=1I6=72I9=1X5=1X4=;84,29,1=1I12=1X3=72I5=1X4=;86,31,1=1I12=1X2=72I1X5=1X4=;86,31,1=1I12=1X1=72I1=1X5=1X4=;86,31,1=1I12=1X72I2=1X5=1X4=;89,4,1=1I12=1D3=73I5=1X4= YP:f:3.16227e-06 -AS:i:62 YM:i:32 YP:f:0.00158239 -AS:i:62 YM:i:37 YA:Z:62,37,5=1X10=1885D84=;62,37,5=1X9=1885D85=;62,37,5=1X8=1885D86=;62,37,5=1X7=1885D87=;62,37,5=1X6=1885D88=;62,37,5=1X5=1885D89=;62,37,5=1X4=1885D90=;62,37,5=1X3=1885D91=;62,37,5=1X2=1885D92= YP:f:6.30957e-07 -AS:i:62 YM:i:37 YA:Z:62,37,5=1X11=307D83=;62,37,5=1X10=307D84=;62,37,5=1X9=307D85=;62,37,5=1X8=307D86=;62,37,5=1X7=307D87=;62,37,5=1X6=307D88=;62,37,5=1X5=307D89=;62,37,5=1X4=307D90=;62,37,5=1X3=307D91=;62,37,5=1X2=307D92=;87,62,5=1X12=1X307D81= YP:f:6.30957e-07 -AS:i:64 YM:i:64 YP:f:3.98103e-07 -AS:i:66 YM:i:66 YP:f:2.51189e-07 -AS:i:7 YM:i:7 YP:f:1 -AS:i:73 YM:i:13 YP:f:1.58489e-06 -AS:i:76 YM:i:21 YA:Z:76,21,4=1X1I9=307D47=1X37=;76,21,4=1X1I8=307D48=1X37=;76,21,4=1X1I7=307D49=1X37=;76,21,4=1X1I6=307D50=1X37=;76,21,4=1X1I5=307D51=1X37=;76,21,4=1X1I4=307D52=1X37=;76,21,4=1X1I3=307D53=1X37=;76,21,4=1X1I2=307D54=1X37=;78,23,4=1X1I10=1X307D45=1X37= YP:f:1.98897e-07 -AS:i:76 YM:i:51 YA:Z:76,51,1=1X6=104D19=1X9=1X12=1X49=;101,76,1=1X7=1X104D17=1X9=1X12=1X49= YP:f:0.00199129 -AS:i:78 YM:i:23 YA:Z:78,23,1=1I1=2X8=27D87=;78,23,1=1I1=2X7=27D88=;78,23,1=1I1=2X6=27D89=;78,23,1=1I1=2X5=27D90=;78,23,1=1I1=2X4=27D91=;78,23,1=1I1=2X3=27D92=;85,0,1=1I1=1I4=28D92=;90,65,1=1X2=1X2=1X1=26D91=;90,65,1=1X2=1X2=1X26D92= YP:f:2.51189e-08 -AS:i:78 YM:i:23 YA:Z:78,23,1=1X7=1134D32=1X56=1I1=;78,23,1=1X6=1134D33=1X56=1I1=;106,51,1=1X8=1X9=1134D21=1X56=1I1=;106,51,1=1X8=1X8=1134D22=1X56=1I1=;106,51,1=1X8=1X7=1134D23=1X56=1I1=;106,51,1=1X8=1X6=1134D24=1X56=1I1=;106,51,1=1X8=1X5=1134D25=1X56=1I1=;106,51,1=1X8=1X4=1134D26=1X56=1I1=;106,51,1=1X8=1X3=1134D27=1X56=1I1=;106,51,1=1X8=1X2=1134D28=1X56=1I1=;106,51,1=1X8=1X1=1134D29=1X56=1I1=;106,51,1=1X8=1X1134D30=1X56=1I1= YP:f:3.11284e-05 -AS:i:84 YM:i:24 YP:f:3.16218e-05 -AS:i:85 YM:i:0 YA:Z:85,0,1=1I1=1I9=15D87=;85,0,1=1I1=1I8=15D88=;85,0,1=1I1=1I7=15D89=;85,0,1=1I1=1I6=15D90=;85,0,1=1I1=1I5=15D91=;85,0,1=1I1=1I4=15D92=;114,59,1=2X1I1X3=14D92= YP:f:3.16228e-09 -AS:i:9 YM:i:9 YP:f:0.996848 -AS:i:91 YM:i:36 YA:Z:91,36,14=1X76=1056D2=1X2=1D4=;92,37,14=1X77=1058D1I1=1X5=;92,37,14=1X76=1058D1=1I1=1X5=;92,37,14=1X75=1058D2=1I1=1X5=;92,37,14=1X74=1058D3=1I1=1X5=;92,37,14=1X73=1058D4=1I1=1X5=;92,37,14=1X72=1058D5=1I1=1X5=;92,37,14=1X71=1058D6=1I1=1X5=;92,37,14=1X70=1058D7=1I1=1X5=;94,69,14=1X77=1057D1X1=1X5= YP:f:1.25893e-09 -AS:i:92 YM:i:37 YA:Z:92,37,3=1I1=1X12=171D82=;92,37,3=1I1=1X11=171D83=;92,37,3=1I1=1X10=171D84=;92,37,3=1I1=1X9=171D85=;92,37,3=1I1=1X8=171D86=;92,37,3=1I1=1X7=171D87=;92,37,3=1I1=1X6=171D88=;92,37,3=1I1=1X5=171D89=;92,37,3=1I1=1X4=171D90=;92,37,3=1I1=1X3=171D91=;92,37,3=1I1=1X2=171D92= YP:f:6.30957e-10 -AS:i:92 YM:i:37 YA:Z:92,37,3=1I1=1X13=1751D81=;92,37,3=1I1=1X12=1751D82=;92,37,3=1I1=1X11=1751D83=;92,37,3=1I1=1X10=1751D84=;92,37,3=1I1=1X9=1751D85=;92,37,3=1I1=1X8=1751D86=;92,37,3=1I1=1X7=1751D87=;92,37,3=1I1=1X6=1751D88=;92,37,3=1I1=1X5=1751D89=;92,37,3=1I1=1X4=1751D90=;92,37,3=1I1=1X3=1751D91=;92,37,3=1I1=1X2=1751D92= YP:f:6.30957e-10 -AS:i:94 YM:i:94 YP:f:1 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