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ssadedin / bazam

A read extraction and realignment tool for next generation sequencing data
GNU Lesser General Public License v2.1
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locating pairs in CRAM stopped working in versions after 1.0.1 #32

Open seru71 opened 1 year ago

seru71 commented 1 year ago

Having BAM and CRAM created from it (samtools view -CT $REFERENCE_FASTA bam > cram I found that although version 1.0.1 works fine both files, more recent versions:

manage to get the reads out of BAM file only. With CRAM input PairScanner processes all the reads, but fails to pair them. Below is the last stderr line on a test files with one pair of reads. Stdout is empty

[...]
PairScanner [1] INFO    |3:12:33 Processed 2 in 0.017 seconds  @ 105.26/s   (1:10040, loc: 2,0,0 chm: 0 shf: 0 fmt: 0, wrote: 0, mem: 0/769.9m/1.1g)

Command used:

java -Dsamjdk.reference_fasta=${REFERENCE_FASTA} -jar [PATH]/bazam.jar -bam [BAM|CRAM]

SAM file to reproduce the issue:

@HD VN:1.6  SO:coordinate
@SQ SN:1    LN:249250621    M5:1b22b98cdeb4a9304cb5d48026a85128 UR:genome.fa
@SQ SN:2    LN:243199373    M5:a0d9851da00400dec1098a9255ac712e UR:genome.fa
@SQ SN:3    LN:198022430    M5:fdfd811849cc2fadebc929bb925902e5 UR:genome.fa
@SQ SN:4    LN:191154276    M5:23dccd106897542ad87d2765d28a19a1 UR:genome.fa
@SQ SN:5    LN:180915260    M5:0740173db9ffd264d728f32784845cd7 UR:genome.fa
@SQ SN:6    LN:171115067    M5:1d3a93a248d92a729ee764823acbbc6b UR:genome.fa
@SQ SN:7    LN:159138663    M5:618366e953d6aaad97dbe4777c29375e UR:genome.fa
@SQ SN:8    LN:146364022    M5:96f514a9929e410c6651697bded59aec UR:genome.fa
@SQ SN:9    LN:141213431    M5:3e273117f15e0a400f01055d9f393768 UR:genome.fa
@SQ SN:10   LN:135534747    M5:988c28e000e84c26d552359af1ea2e1d UR:genome.fa
@SQ SN:11   LN:135006516    M5:98c59049a2df285c76ffb1c6db8f8b96 UR:genome.fa
@SQ SN:12   LN:133851895    M5:51851ac0e1a115847ad36449b0015864 UR:genome.fa
@SQ SN:13   LN:115169878    M5:283f8d7892baa81b510a015719ca7b0b UR:genome.fa
@SQ SN:14   LN:107349540    M5:98f3cae32b2a2e9524bc19813927542e UR:genome.fa
@SQ SN:15   LN:102531392    M5:e5645a794a8238215b2cd77acb95a078 UR:genome.fa
@SQ SN:16   LN:90354753 M5:fc9b1a7b42b97a864f56b348b06095e6 UR:genome.fa
@SQ SN:17   LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:genome.fa
@SQ SN:18   LN:78077248 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c UR:genome.fa
@SQ SN:19   LN:59128983 M5:1aacd71f30db8e561810913e0b72636d UR:genome.fa
@SQ SN:20   LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:genome.fa
@SQ SN:21   LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:genome.fa
@SQ SN:22   LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:genome.fa
@SQ SN:X    LN:155270560    M5:7e0e2e580297b7764e31dbc80c2540dd UR:genome.fa
@SQ SN:Y    LN:59373566 M5:1fa3474750af0948bdf97d5a0ee52e51 UR:genome.fa
@SQ SN:MT   LN:16569    M5:c68f52674c9fb33aef52dcf399755519 UR:genome.fa
@SQ SN:GL000207.1   LN:4262 M5:f3814841f1939d3ca19072d9e89f3fd7 UR:genome.fa
@SQ SN:GL000226.1   LN:15008    M5:1c1b2cd1fccbc0a99b6a447fa24d1504 UR:genome.fa
@SQ SN:GL000229.1   LN:19913    M5:d0f40ec87de311d8e715b52e4c7062e1 UR:genome.fa
@SQ SN:GL000231.1   LN:27386    M5:ba8882ce3a1efa2080e5d29b956568a4 UR:genome.fa
@SQ SN:GL000210.1   LN:27682    M5:851106a74238044126131ce2a8e5847c UR:genome.fa
@SQ SN:GL000239.1   LN:33824    M5:99795f15702caec4fa1c4e15f8a29c07 UR:genome.fa
@SQ SN:GL000235.1   LN:34474    M5:118a25ca210cfbcdfb6c2ebb249f9680 UR:genome.fa
@SQ SN:GL000201.1   LN:36148    M5:dfb7e7ec60ffdcb85cb359ea28454ee9 UR:genome.fa
@SQ SN:GL000247.1   LN:36422    M5:7de00226bb7df1c57276ca6baabafd15 UR:genome.fa
@SQ SN:GL000245.1   LN:36651    M5:89bc61960f37d94abf0df2d481ada0ec UR:genome.fa
@SQ SN:GL000197.1   LN:37175    M5:6f5efdd36643a9b8c8ccad6f2f1edc7b UR:genome.fa
@SQ SN:GL000203.1   LN:37498    M5:96358c325fe0e70bee73436e8bb14dbd UR:genome.fa
@SQ SN:GL000246.1   LN:38154    M5:e4afcd31912af9d9c2546acf1cb23af2 UR:genome.fa
@SQ SN:GL000249.1   LN:38502    M5:1d78abec37c15fe29a275eb08d5af236 UR:genome.fa
@SQ SN:GL000196.1   LN:38914    M5:d92206d1bb4c3b4019c43c0875c06dc0 UR:genome.fa
@SQ SN:GL000248.1   LN:39786    M5:5a8e43bec9be36c7b49c84d585107776 UR:genome.fa
@SQ SN:GL000244.1   LN:39929    M5:0996b4475f353ca98bacb756ac479140 UR:genome.fa
@SQ SN:GL000238.1   LN:39939    M5:131b1efc3270cc838686b54e7c34b17b UR:genome.fa
@SQ SN:GL000202.1   LN:40103    M5:06cbf126247d89664a4faebad130fe9c UR:genome.fa
@SQ SN:GL000234.1   LN:40531    M5:93f998536b61a56fd0ff47322a911d4b UR:genome.fa
@SQ SN:GL000232.1   LN:40652    M5:3e06b6741061ad93a8587531307057d8 UR:genome.fa
@SQ SN:GL000206.1   LN:41001    M5:43f69e423533e948bfae5ce1d45bd3f1 UR:genome.fa
@SQ SN:GL000240.1   LN:41933    M5:445a86173da9f237d7bcf41c6cb8cc62 UR:genome.fa
@SQ SN:GL000236.1   LN:41934    M5:fdcd739913efa1fdc64b6c0cd7016779 UR:genome.fa
@SQ SN:GL000241.1   LN:42152    M5:ef4258cdc5a45c206cea8fc3e1d858cf UR:genome.fa
@SQ SN:GL000243.1   LN:43341    M5:cc34279a7e353136741c9fce79bc4396 UR:genome.fa
@SQ SN:GL000242.1   LN:43523    M5:2f8694fc47576bc81b5fe9e7de0ba49e UR:genome.fa
@SQ SN:GL000230.1   LN:43691    M5:b4eb71ee878d3706246b7c1dbef69299 UR:genome.fa
@SQ SN:GL000237.1   LN:45867    M5:e0c82e7751df73f4f6d0ed30cdc853c0 UR:genome.fa
@SQ SN:GL000233.1   LN:45941    M5:7fed60298a8d62ff808b74b6ce820001 UR:genome.fa
@SQ SN:GL000204.1   LN:81310    M5:efc49c871536fa8d79cb0a06fa739722 UR:genome.fa
@SQ SN:GL000198.1   LN:90085    M5:868e7784040da90d900d2d1b667a1383 UR:genome.fa
@SQ SN:GL000208.1   LN:92689    M5:aa81be49bf3fe63a79bdc6a6f279abf6 UR:genome.fa
@SQ SN:GL000191.1   LN:106433   M5:d75b436f50a8214ee9c2a51d30b2c2cc UR:genome.fa
@SQ SN:GL000227.1   LN:128374   M5:a4aead23f8053f2655e468bcc6ecdceb UR:genome.fa
@SQ SN:GL000228.1   LN:129120   M5:c5a17c97e2c1a0b6a9cc5a6b064b714f UR:genome.fa
@SQ SN:GL000214.1   LN:137718   M5:46c2032c37f2ed899eb41c0473319a69 UR:genome.fa
@SQ SN:GL000221.1   LN:155397   M5:3238fb74ea87ae857f9c7508d315babb UR:genome.fa
@SQ SN:GL000209.1   LN:159169   M5:f40598e2a5a6b26e84a3775e0d1e2c81 UR:genome.fa
@SQ SN:GL000218.1   LN:161147   M5:1d708b54644c26c7e01c2dad5426d38c UR:genome.fa
@SQ SN:GL000220.1   LN:161802   M5:fc35de963c57bf7648429e6454f1c9db UR:genome.fa
@SQ SN:GL000213.1   LN:164239   M5:9d424fdcc98866650b58f004080a992a UR:genome.fa
@SQ SN:GL000211.1   LN:166566   M5:7daaa45c66b288847b9b32b964e623d3 UR:genome.fa
@SQ SN:GL000199.1   LN:169874   M5:569af3b73522fab4b40995ae4944e78e UR:genome.fa
@SQ SN:GL000217.1   LN:172149   M5:6d243e18dea1945fb7f2517615b8f52e UR:genome.fa
@SQ SN:GL000216.1   LN:172294   M5:642a232d91c486ac339263820aef7fe0 UR:genome.fa
@SQ SN:GL000215.1   LN:172545   M5:5eb3b418480ae67a997957c909375a73 UR:genome.fa
@SQ SN:GL000205.1   LN:174588   M5:d22441398d99caf673e9afb9a1908ec5 UR:genome.fa
@SQ SN:GL000219.1   LN:179198   M5:f977edd13bac459cb2ed4a5457dba1b3 UR:genome.fa
@SQ SN:GL000224.1   LN:179693   M5:d5b2fc04f6b41b212a4198a07f450e20 UR:genome.fa
@SQ SN:GL000223.1   LN:180455   M5:399dfa03bf32022ab52a846f7ca35b30 UR:genome.fa
@SQ SN:GL000195.1   LN:182896   M5:5d9ec007868d517e73543b005ba48535 UR:genome.fa
@SQ SN:GL000212.1   LN:186858   M5:563531689f3dbd691331fd6c5730a88b UR:genome.fa
@SQ SN:GL000222.1   LN:186861   M5:6fe9abac455169f50470f5a6b01d0f59 UR:genome.fa
@SQ SN:GL000200.1   LN:187035   M5:75e4c8d17cd4addf3917d1703cacaf25 UR:genome.fa
@SQ SN:GL000193.1   LN:189789   M5:dbb6e8ece0b5de29da56601613007c2a UR:genome.fa
@SQ SN:GL000194.1   LN:191469   M5:6ac8f815bf8e845bb3031b73f812c012 UR:genome.fa
@SQ SN:GL000225.1   LN:211173   M5:63945c3e6962f28ffd469719a747e73c UR:genome.fa
@SQ SN:GL000192.1   LN:547496   M5:325ba9e808f669dfeee210fdd7b470ac UR:genome.fa
@SQ SN:NC_007605    LN:171823   M5:6743bd63b3ff2b5b8985d8933c53290a UR:genome.fa
@SQ SN:hs37d5   LN:35477943 M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1 UR:genome.fa
A00125:159:HF2KTDSXX:1:1135:1561:28369  81  1   9996    0   76S75M  =   10040   -31 CCCTCACCCTACCCTTTTCACGAAGACGACGGCATACGCGATACATAGCGGTGACGGTAGTTCTGACGCTTGCTCTTCCGATCACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC FFF,:,F::,:,F:,F,:F,,,,:,F,,F,,,F,,FF,,,F::F,F,,F,:::FF,,,F,,,F:,FF:,,::F,:FFFFF,F,,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFF NM:i:1  MD:Z:6A68   MC:Z:72M79S AS:i:70 XS:i:70
A00125:159:HF2KTDSXX:1:1135:1561:28369  161 1   10040   0   72M79S  =   9996    31  CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACGCAAGAGCCTCGGCGTGGGCCAGACGCTAGGACGGAGCGTAACGCTAGGGCTGCGCCGGAGCCTTACCCTCAGCGGGGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF,,,:,,,,,,:,F,FF,,,,,,,,,:,,F,,,:,,,,FF,,,,,F,,,,,:,,,,,,,,:F,F,,,,,:,,,,,,,,:,,F:,: MC:Z:76S75M AS:i:72 XS:i:69 MD:Z:72 NM:i:0
shaze commented 1 year ago

Yes, I've experienced the same issue. The program seems to process all the files but there's no output

This is a real pity -- the older version doesn't support extraction of the original quality scores so it's not usable as is without first converting to BAM using samtools. Since this needs to go to disk since Bazam needs an index, it defeats the purpose.

It would be great to have this fixed.